Bio-Tools-Phylo-PAML-1.7.3/0000755000175000017500000000000013316145226016154 5ustar carandraugcarandraugBio-Tools-Phylo-PAML-1.7.3/Changes0000644000175000017500000000162013316145226017446 0ustar carandraugcarandraugSummary of important user-visible changes for Bio-Tools-Phylo-PAML ------------------------------------------------------------------ 1.7.3 2018-07-01 13:35:29+01:00 Europe/London * Bio::Installer::PAML has been removed. Not only did it no longer work, it was also unsecure. Either install PAML via your system package manager, or download it from upstream, currently at http://abacus.gene.ucl.ac.uk/software/paml.html * Check for the presence of paml programs now happens during build instead of during the test phase. This avoids failure reports from CPAN Testers. * Fixed reading of results for at least codeml and yno00 in cases where next_result was previously returning undef. May be specific to PAML version 4.8 and 4.9 (current PAML version). 1.7.2 2017-09-11 19:11:43+01:00 Europe/London * First release after split from bioperl-live and bioperl-run. Bio-Tools-Phylo-PAML-1.7.3/dist.ini0000644000175000017500000000051513316145226017621 0ustar carandraugcarandraugname = Bio-Tools-Phylo-PAML version = 1.7.3 author = Aaron J Mackey author = Jason Stajich copyright_holder = Aaron J Mackey , Jason Stajich license = Perl_5 [@BioPerl] [CheckBin] command = codeml command = yn00 command = basemlg command = evolver Bio-Tools-Phylo-PAML-1.7.3/LICENSE0000644000175000017500000004413613316145226017171 0ustar carandraugcarandraugThis software is copyright (c) 2018 by Aaron J Mackey , Jason Stajich . This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself. Terms of the Perl programming language system itself a) the GNU General Public License as published by the Free Software Foundation; either version 1, or (at your option) any later version, or b) the "Artistic License" --- The GNU General Public License, Version 1, February 1989 --- This software is Copyright (c) 2018 by Aaron J Mackey , Jason Stajich . This is free software, licensed under: The GNU General Public License, Version 1, February 1989 GNU GENERAL PUBLIC LICENSE Version 1, February 1989 Copyright (C) 1989 Free Software Foundation, Inc. 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The license agreements of most software companies try to keep users at the mercy of those companies. 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This License Agreement applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any work containing the Program or a portion of it, either verbatim or with modifications. Each licensee is addressed as "you". 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this General Public License and to the absence of any warranty; and give any other recipients of the Program a copy of this General Public License along with the Program. You may charge a fee for the physical act of transferring a copy. 2. 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The End Bio-Tools-Phylo-PAML-1.7.3/t/0000755000175000017500000000000013316145226016417 5ustar carandraugcarandraugBio-Tools-Phylo-PAML-1.7.3/t/PAML-run.t0000644000175000017500000001147013316145226020142 0ustar carandraugcarandraug#!/usr/bin/env perl use utf8; use strict; use warnings; use Test::More; use File::Spec; use Bio::AlignIO; use Bio::TreeIO; use Bio::Tools::Phylo::PAML; use Bio::Tools::Run::Phylo::PAML::Codeml; use Bio::Tools::Run::Phylo::PAML::Yn00; sub test_input_file { return File::Spec->catfile('t', 'data', @_); } my $verbose = 0; my $inpaml = Bio::Tools::Phylo::PAML->new(-file => test_input_file('codeml.mlc')); ok($inpaml); my $codeml = Bio::Tools::Run::Phylo::PAML::Codeml->new (-params => {'runmode' => -2, 'seqtype' => 1, 'model' => 0, 'alpha' => '0', 'omega' => 0.4, 'kappa' => 2, 'CodonFreq'=> 2, 'NSsites' => 0, 'model' => 0, }, -verbose => $verbose); my $in = Bio::AlignIO->new(-format => 'phylip', -file => test_input_file('gf-s85.phylip')); my $aln = $in->next_aln; $codeml->alignment($aln); my ($rc,$results) = $codeml->run(); is($rc,1); ok(defined $results, "got results"); my $result = $results->next_result; ok(defined $result, "got a result"); my $MLmatrix = $result->get_MLmatrix; my ($vnum) = ($result->version =~ /(\d+(\.\d+)?)/); SKIP: { if( $vnum == 3.12 ) { # PAML 2.12 results is($MLmatrix->[0]->[1]->{'dN'}, 0.0693); is($MLmatrix->[0]->[1]->{'dS'},1.1459); is($MLmatrix->[0]->[1]->{'omega'}, 0.0605); is($MLmatrix->[0]->[1]->{'S'}, 273.5); is($MLmatrix->[0]->[1]->{'N'}, 728.5); is($MLmatrix->[0]->[1]->{'t'}, 1.0895); skip($MLmatrix->[0]->[1]->{'lnL'}, "I don't know what this should be, if you run this part, email the list so we can update the value", 1); } elsif( $vnum >= 3.13 && $vnum < 4) { # PAML 2.13 results is($MLmatrix->[0]->[1]->{'dN'}, 0.0713); is($MLmatrix->[0]->[1]->{'dS'},1.2462); is(sprintf("%.4f",$MLmatrix->[0]->[1]->{'omega'}), 0.0572); is($MLmatrix->[0]->[1]->{'S'}, 278.8); is($MLmatrix->[0]->[1]->{'N'}, 723.2); is(sprintf("%.4f",$MLmatrix->[0]->[1]->{'t'}), 1.1946); skip($MLmatrix->[0]->[1]->{'lnL'}, "I don't know what this should be, if you run this part, email the list so we can update the value", 1); } elsif( $vnum >= 4 ) { ## PAML 4, 4.8, and 4.9h results is($MLmatrix->[0]->[1]->{'dN'}, 0.0713); is($MLmatrix->[0]->[1]->{'dS'},1.2462); is(sprintf("%.4f",$MLmatrix->[0]->[1]->{'omega'}), 0.0572); is($MLmatrix->[0]->[1]->{'S'}, 278.8); is($MLmatrix->[0]->[1]->{'N'}, 723.2); is(sprintf("%.4f",$MLmatrix->[0]->[1]->{'t'}), 1.1946); is($MLmatrix->[0]->[1]->{'lnL'}, -1929.935243); } else { skip("Can't test the result output, don't know about PAML version ".$result->version, 7); } } unlike($codeml->error_string, qr/Error/); # we don't expect any errors; my $yn00 = Bio::Tools::Run::Phylo::PAML::Yn00->new(); $yn00->alignment($aln); ($rc,$results) = $yn00->run(); is($rc,1); ok(defined $results, "got results"); $result = $results->next_result; ok(defined $result, "got a result"); $MLmatrix = $result->get_MLmatrix; is($MLmatrix->[0]->[1]->{'dN'}, 0.0846); is($MLmatrix->[0]->[1]->{'dS'}, 1.0926); is($MLmatrix->[0]->[1]->{'omega'}, 0.0774); is($MLmatrix->[0]->[1]->{'S'}, 278.4); is($MLmatrix->[0]->[1]->{'N'}, 723.6); is($MLmatrix->[0]->[1]->{'t'}, 1.0941); unlike($yn00->error_string, qr/Error/); # we don't expect any errors; $codeml = Bio::Tools::Run::Phylo::PAML::Codeml->new (-params => { 'alpha' => 1.53 }, -verbose => $verbose); ok($codeml); # AAML my $cysaln = Bio::AlignIO->new(-format => 'msf', -file => test_input_file('cysprot.msf'))->next_aln; my $cystre = Bio::TreeIO->new(-format => 'newick', -file => test_input_file('cysprot.raxml.tre'))->next_tree; ok($cysaln); ok($cystre); $codeml = Bio::Tools::Run::Phylo::PAML::Codeml->new ( -verbose => 0, -tree => $cystre, -params => { 'runmode' => 0, # provide a usertree 'seqtype' => 2, # AMINO ACIDS, 'model' => 0, # one dN/dS rate 'NSsites' => 0, # one -- swap this with 1, 2, 3 etc 'clock' => 0, # 0 = no clock 'getSE' => 1, # get Standard Error 'fix_blength' => 0, # use initial BLengths 'ncatG' => 1, #increase approrpriately for NSsites, }, -alignment => $cysaln, -save_tempfiles => 1, ); ok($codeml); ($rc,$results) = $codeml->run(); is($rc,1); ok(defined $results, "got results"); $result = $results->next_result; ($vnum) = ($result->version =~ /(\d+(\.\d+)?)/); for my $tree ( $result->get_trees ) { my $node = $tree->find_node(-id => 'CATL_HUMAN'); if( $vnum == 4 ) { is($node->branch_length, '0.216223'); } else { is($node->branch_length, '0.216223'); } } done_testing (); Bio-Tools-Phylo-PAML-1.7.3/t/author-mojibake.t0000644000175000017500000000035313316145226021666 0ustar carandraugcarandraug#!perl BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } use strict; use warnings qw(all); use Test::More; use Test::Mojibake; all_files_encoding_ok(); Bio-Tools-Phylo-PAML-1.7.3/t/author-pod-coverage.t0000644000175000017500000000053613316145226022463 0ustar carandraugcarandraug#!perl BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } # This file was automatically generated by Dist::Zilla::Plugin::PodCoverageTests. use Test::Pod::Coverage 1.08; use Pod::Coverage::TrustPod; all_pod_coverage_ok({ coverage_class => 'Pod::Coverage::TrustPod' }); Bio-Tools-Phylo-PAML-1.7.3/t/00-compile.t0000644000175000017500000000576313316145226020464 0ustar carandraugcarandrauguse 5.006; use strict; use warnings; # this test was generated with Dist::Zilla::Plugin::Test::Compile 2.058 use Test::More; plan tests => 9 + ($ENV{AUTHOR_TESTING} ? 1 : 0); my @module_files = ( 'Bio/Tools/Phylo/PAML.pm', 'Bio/Tools/Phylo/PAML/Codeml.pm', 'Bio/Tools/Phylo/PAML/ModelResult.pm', 'Bio/Tools/Phylo/PAML/Result.pm', 'Bio/Tools/Run/Phylo/PAML/Baseml.pm', 'Bio/Tools/Run/Phylo/PAML/Codeml.pm', 'Bio/Tools/Run/Phylo/PAML/Evolver.pm', 'Bio/Tools/Run/Phylo/PAML/Yn00.pm' ); my @scripts = ( 'bin/bp_pairwise_kaks' ); # no fake home requested my @switches = ( -d 'blib' ? '-Mblib' : '-Ilib', ); use File::Spec; use IPC::Open3; use IO::Handle; open my $stdin, '<', File::Spec->devnull or die "can't open devnull: $!"; my @warnings; for my $lib (@module_files) { # see L my $stderr = IO::Handle->new; diag('Running: ', join(', ', map { my $str = $_; $str =~ s/'/\\'/g; q{'} . $str . q{'} } $^X, @switches, '-e', "require q[$lib]")) if $ENV{PERL_COMPILE_TEST_DEBUG}; my $pid = open3($stdin, '>&STDERR', $stderr, $^X, @switches, '-e', "require q[$lib]"); binmode $stderr, ':crlf' if $^O eq 'MSWin32'; my @_warnings = <$stderr>; waitpid($pid, 0); is($?, 0, "$lib loaded ok"); shift @_warnings if @_warnings and $_warnings[0] =~ /^Using .*\bblib/ and not eval { +require blib; blib->VERSION('1.01') }; if (@_warnings) { warn @_warnings; push @warnings, @_warnings; } } foreach my $file (@scripts) { SKIP: { open my $fh, '<', $file or warn("Unable to open $file: $!"), next; my $line = <$fh>; close $fh and skip("$file isn't perl", 1) unless $line =~ /^#!\s*(?:\S*perl\S*)((?:\s+-\w*)*)(?:\s*#.*)?$/; @switches = (@switches, split(' ', $1)) if $1; close $fh and skip("$file uses -T; not testable with PERL5LIB", 1) if grep { $_ eq '-T' } @switches and $ENV{PERL5LIB}; my $stderr = IO::Handle->new; diag('Running: ', join(', ', map { my $str = $_; $str =~ s/'/\\'/g; q{'} . $str . q{'} } $^X, @switches, '-c', $file)) if $ENV{PERL_COMPILE_TEST_DEBUG}; my $pid = open3($stdin, '>&STDERR', $stderr, $^X, @switches, '-c', $file); binmode $stderr, ':crlf' if $^O eq 'MSWin32'; my @_warnings = <$stderr>; waitpid($pid, 0); is($?, 0, "$file compiled ok"); shift @_warnings if @_warnings and $_warnings[0] =~ /^Using .*\bblib/ and not eval { +require blib; blib->VERSION('1.01') }; # in older perls, -c output is simply the file portion of the path being tested if (@_warnings = grep { !/\bsyntax OK$/ } grep { chomp; $_ ne (File::Spec->splitpath($file))[2] } @_warnings) { warn @_warnings; push @warnings, @_warnings; } } } is(scalar(@warnings), 0, 'no warnings found') or diag 'got warnings: ', ( Test::More->can('explain') ? Test::More::explain(\@warnings) : join("\n", '', @warnings) ) if $ENV{AUTHOR_TESTING}; Bio-Tools-Phylo-PAML-1.7.3/t/author-no-tabs.t0000644000175000017500000000161213316145226021447 0ustar carandraugcarandraug BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } use strict; use warnings; # this test was generated with Dist::Zilla::Plugin::Test::NoTabs 0.15 use Test::More 0.88; use Test::NoTabs; my @files = ( 'bin/bp_pairwise_kaks', 'lib/Bio/Tools/Phylo/PAML.pm', 'lib/Bio/Tools/Phylo/PAML/Codeml.pm', 'lib/Bio/Tools/Phylo/PAML/ModelResult.pm', 'lib/Bio/Tools/Phylo/PAML/Result.pm', 'lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm', 'lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm', 'lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm', 'lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm', 't/00-compile.t', 't/PAML-parser.t', 't/PAML-run.t', 't/author-eol.t', 't/author-mojibake.t', 't/author-no-tabs.t', 't/author-pod-coverage.t', 't/author-pod-syntax.t' ); notabs_ok($_) foreach @files; done_testing; Bio-Tools-Phylo-PAML-1.7.3/t/author-pod-syntax.t0000644000175000017500000000045413316145226022215 0ustar carandraugcarandraug#!perl BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } # This file was automatically generated by Dist::Zilla::Plugin::PodSyntaxTests. use strict; use warnings; use Test::More; use Test::Pod 1.41; all_pod_files_ok(); Bio-Tools-Phylo-PAML-1.7.3/t/data/0000755000175000017500000000000013316145226017330 5ustar carandraugcarandraugBio-Tools-Phylo-PAML-1.7.3/t/data/baseml.pairwise0000644000175000017500000000164113316145226022342 0ustar carandraugcarandraug seed used = 30455833 BASEML (in paml 3.14, January 2004) m.phy HKY85 dGamma (ncatG=5) ns = 3 ls = 57 # site patterns = 12 7 16 15 1 3 2 1 1 8 1 1 1 wih99_snap GTAGAGTACT TT wm276_snap ...AGAG..G A. jec21_snap ....GACT.. CC Frequencies.. T C A G wih99_snap 0.3509 0.1404 0.3333 0.1754 wm276_snap 0.2982 0.1404 0.3509 0.2105 jec21_snap 0.3158 0.1930 0.2982 0.1930 Average 0.3216 0.1579 0.3275 0.1930 # constant sites: 46 (80.70%) ln Lmax (unconstrained) = -110.532715 Distances:HKY85 (kappa) (alpha set at 0.50) This matrix is not used in later m.l. analysis. wih99_snap wm276_snap 0.3240( 9.3595) jec21_snap 0.2974(33.1197) 0.1343( 1.1101) Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml.mlc0000644000175000017500000000712613316145226021276 0ustar carandraugcarandraugAAML (in paml 3.12 February 2002) stewart.aa Model: Empirical (wag.dat) ns = 6 ls = 130 # site patterns = 98 4 1 1 1 1 8 2 1 6 1 1 3 1 1 1 1 1 4 2 1 1 3 1 4 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 1 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Langur KIFERCELAR TLKLGLDGYK VSNWVLAKWG NTETYNPGDE TDYIFQSRYN NGTPGAVDAH ISSALQNNIA DAVARVVSDP QIRVRNHQNK VSQVKGGV Baboon .......... ..R......R I........D ..Q......Q .......H.. D......N.. ..N...D..T .......... .........R ....Q... Human .V........ ..R..M...R I...M..... ..R...A..R .......... D......N.. L.....D... .......R.. ......R..R .R..Q... Rat .TY....F.. ..RN.MS..Y ..D....QHN ..QR.D...Q .......... D...R.KN.G .P....DD.T Q.IQ...R.. ....QR.K.R L.GIRN.. Cow .V........ .......... ....L.T..S ..K....SS. .......KW. D...N...G. V..EME.D.. K...KI..E- ..T.KS.RDH ..S.E.TL Horse .V.SK....H K.AQEM..FG Y....M.EYN ..RFGKNANG S..L..NKWK DN-RSSSN.N .M.K.DE..D .DIS...R.. KMSKVK.KD. L.ELASNL Frequencies.. A R N D C Q E G H I L K M F P S T W Y V Langur 0.1000 0.0462 0.0846 0.0538 0.0615 0.0385 0.0385 0.0846 0.0154 0.0462 0.0615 0.0692 0.0000 0.0154 0.0231 0.0615 0.0385 0.0385 0.0462 0.0769 Baboon 0.0923 0.0615 0.0846 0.0692 0.0615 0.0615 0.0231 0.0769 0.0231 0.0538 0.0615 0.0385 0.0000 0.0154 0.0231 0.0538 0.0462 0.0385 0.0462 0.0692 Human 0.1077 0.1077 0.0769 0.0615 0.0615 0.0462 0.0231 0.0846 0.0077 0.0385 0.0615 0.0385 0.0154 0.0154 0.0154 0.0462 0.0385 0.0385 0.0462 0.0692 Rat 0.0846 0.0923 0.0692 0.0692 0.0615 0.0692 0.0231 0.0769 0.0154 0.0538 0.0462 0.0462 0.0077 0.0154 0.0308 0.0538 0.0462 0.0308 0.0615 0.0462 Cow 0.0775 0.0233 0.0620 0.0543 0.0620 0.0155 0.0620 0.0620 0.0233 0.0388 0.0698 0.0930 0.0078 0.0155 0.0155 0.1008 0.0620 0.0465 0.0388 0.0698 Horse 0.0853 0.0310 0.1008 0.0775 0.0620 0.0155 0.0465 0.0543 0.0155 0.0233 0.0775 0.1163 0.0310 0.0388 0.0078 0.1008 0.0078 0.0388 0.0310 0.0388 Average 0.0913 0.0604 0.0797 0.0643 0.0617 0.0411 0.0360 0.0733 0.0167 0.0424 0.0630 0.0668 0.0103 0.0193 0.0193 0.0694 0.0398 0.0386 0.0450 0.0617 (Ambiguity characters are used to calculate freqs.) # constant sites: 46 (35.38%) AA distances (raw proportions of different sites) Langur Baboon 0.1077 Human 0.1385 0.1077 Rat 0.2923 0.2538 0.2846 Cow 0.2462 0.3000 0.3154 0.4231 Horse 0.5000 0.5000 0.4923 0.4923 0.5462 TREE # 1: (((1, 2), 3), 4, (5, 6)); MP score: -1 lnL(ntime: 9 np: 9): -1042.768973 +0.000000 7..8 8..9 9..1 9..2 8..3 7..4 7..10 10..5 10..6 0.00950 0.02220 0.08009 0.03337 0.06233 0.27133 0.09393 0.24105 0.58792 tree length = 1.40172 (((1:0.080088, 2:0.033370):0.022202, 3:0.062325):0.009497, 4:0.271333, (5:0.241055, 6:0.587920):0.093926); (((Langur:0.080088, Baboon:0.033370):0.022202, Human:0.062325):0.009497, Rat:0.271333, (Cow:0.241055, Horse:0.587920):0.093926); Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml_parse.mlc0000644000175000017500000003133213316145226022464 0ustar carandraugcarandraugCODONML (in paml 3.12 February 2002) abglobin.nuc Model: several dN/dS ratios for branches Codon frequencies: F3x4 ns = 5 ls = 285 # site patterns = 223 9 2 1 1 1 4 3 1 1 1 2 1 1 3 1 7 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 5 1 1 1 4 2 2 1 6 1 1 1 1 1 3 1 1 3 1 1 1 2 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 1 6 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 2 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 2 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 human GTG CTG TCT CCT GCC GAC AAG ACC AAC GTC AAG GCC GCC TGG GGC AAG GTT GGC GCG CAC GCT GGC GAG TAT GGT GCG GAG GCC CTG GAG AGG ATG TTC CTG TCC CCC ACC ACC TAC CCG CAC TTC GAC CTG AGC CAC GGC TCT GCC CAG GTT AAG GGC CAC GGC AAG GTG GCC GAC GCG CTG ACC AAC GCC GTG GCG GTG GAC ATG CCC AAC GCG CTG TCC GCC CTG AGC CTG CAC GCG CTT CGG GAC CCG GTC AAC TTC CTC CTA AGC TGC CTG CTG GCC GCC CTC CCC GCC GAG TTC ACC CCT GCG GTG CAC GCC TCC CTG GCT TCT AGC ACC TCC AAA TAC CGT CTG ACT CCT GAG GAG TCT GCC GTT ACT GCC CTG GGC AAC GTG GAT GAA GTT GGT GGT CTG AGG CTG GTG GTC CCT ACC CAG TTC TTT GAG TCC TTT GGG GAT CTG TCC ACT CCT GAT GCT GTT ATG GGC AAC CCT GTG AAG GCT CAT AAG AAA CTC GGT GCC TTT AGT GAT GGC CTG GCT CAC CTG GAC AAC CTC AAG TTT GCC ACA CTG AGT GAG TGT CAC GAT CCT AAC AGG CTC GGC AAC GTG CTG GTC TGT GTG GCC CAT CAC TTT AAA GAA TTC ACC CCA CCA GTG GCT GCC TAT GTG GGT AAT GCC AAG TAT CAC goat-cow ... ... ... G.C ... ... ... T.. ..T ... ... ... ... ... ... ... ... ... .GC A.. ... ..A .CT ... ..C ..A ... ..T ... ... ... ... ... ... AG. ... ... ... ... ..C ... ... ... ... ... ... ... ..G ... ... ..C ... ... ... ... G.. ... ... .C. ... ... ... ..A ..G ... .GC C.. ... C.. ... GGT A.T ... ..T .AT ... ..T ... ... ..C ..G ..T ... ... ... ... ..T ..T ..G ... .C. ... ... ... TG. ... ... AAT ..T ... ... ..C ... ..C ... ... ... T.. ..C AAC ... ... ... ... ... ... ... ... G.. ... ... G.. ... ..C ..C ... T.T ... ..A ... ... ... ... ... ... ... ... ... ..T ... ..C ..T ... ... ... ... ... ... ... ..C T.. ... ... G.. ... ... ... ... AA. ... ... ... ... ..C ... ... ..G ..A .A. T.. ... ... A.. ... A.. AAG ..T ..C ..T G.. ... ... ... ..T G.G ... ... ... ... ..T ... ... ... .A. ... ... ... ... ..A ..G GT. ... ..T .GC A.T ... ..G ... ... ... ..G GTG C.. ... .A. .T. ... ... ... ... .GA ... ..T rabbit ... ... ... ..C ..T ... ... ... ... A.. ... A.T ... ... .AA ... A.C ... AGC ... .G. ... ... ... ..C ..C ... ... G.. ... ... ... ... T.. GG. ... ... ... ... ..C ... ... ... T.C .C. ... ... ... .AG ... A.C ..A .C. ... ... ... ... T.. ..A ..C ... ... ..G ... ... .GC C.. ... C.. ... GG. ..C ... ..T A.T ..C ... ... ... ... ..G ... ... ... ..G ..T ... ... ..G TC. ... ... ... ... AA. .A. ... AGT ..A ... ... ... ... ... ..T ... ... ... ..C AAC ... ... ... ... ..T ... ... T.C AG. ... ... ... ..G ..C ... ... ... ... ..T ... ..A ... ... ... ... ... ... ... ..T ... ..A ... ... ... ..C ... ... ... ... ..C ... ... T.. G.A A.. ... ... ... AA. ..T ... ... ... ... ... ... ..G ..G .C. ... ..C ... ..G ..T ... AG. ... ... ... ... ... ..A ... ..T .AG ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ..T AT. ... T.T ... ..T ... ... ... ... ..T ..T .AG ... ... ... ... ... ... ... ..T ..A ..C ... rat ... ..C ... G.A .AT ... ..A ... ... A.. ... AA. TG. ... ..G ... A.. ..T .GC ..T .G. ..T ..A ... ..C .A. ... ... ..A C.. ... ... ... GCT G.. ... ... ... ... T.T ... A.T ..T G.A ... .C. ... ... ... ... ..C ... .CT ... ... ... ..T ..T ..T ..C T.. G.. ..A ..T .CA .AC ..C ..A C.. ..T GGT ..C ... ... A.T ... ... ... ..T ..C ..G ..T ..T ..T ... ... ... T.. ..G ... ... ... T.. ..T TG. .A. ..T .GA ..T ... ..A ..C ..C A.. ... ... ..T ..T ..C ... ... ..T ... ..G ... ... ..A ... GA. .CT ... G.. ..T ... .A. ... ... ..A ... CCT ... ..T ... ... ..C ... ... ... ..T ... ... ... ... .A. ... ..T AG. ... ... ..C ... ... T.. G.C TC. ... A.C ... ..T ... ... ... ... ..C ... ... ..G A.A AAC ... ..C .A. ... ... ... AAA ... T.. ... ... ... ... ... ..T CAT ... ... ..A ... ..T ... ... ... ... ... ... ..T A.. A.T ..G AT. ... .G. ..C ... C.G ..G ... ... ... ..C TGT .CA ... ... .TC ... ..A .G. ..T ... ..C ... marsupial ... ..C ..G GA. ..T ... ... ..T C.. ..G ..A ... AT. ... ..T ... ..G ..A .GC ... ..C ..T .CC ..C .CA ..T ..A ..T ..T .CC ..A .CC ... ..C ... ... ..T ... ... ..C ... ... ... ... TC. .C. ... ..C ... ... A.C C.. ..T ..T ..T ... ..A ... ..T ..C ..T T.. C.G ..T ..T ..C C.. ... C.. ... GGA A.C A.. ... AAA ..A ... ... ... ..C ..G A.A ..T ..C ..G ... ... ... ..C TCT ... A.C ... ... ... ..G AG. AAG ..T ..G ..T ..C .AA ... ... ... ... T.T ..C ... GCT ... ..G ..G ... ... T.. ... T.. ... ... AAC TG. A.C ... A.. A.C TCT C.G ..T ..C C.G AC. ... ... ..T ... ..C ..T ... ..C ... ACC ..T ... .G. AG. ... ..T ... ... ... T.. ... .GC ... ..C ... TCA ..T T.. ..T C.A ..C ... GCT ..G T.G ACC T.. ..C G.. ..A .CA G.C AAG ..T T.. ... ... ..G ... .A. ... .AG T.. ... ... ... ..T ..C ... ... .A. A.G ..G ..T A.C A.T ..G ATC TGC ..T G.G ... ... ..G ..T ..T ..T ..T GA. TGT .T. ..T .GG C.C ..A C.. ... ... ..C ... Codon usage in sequences -------------------------------------------------------------------------------------------------- Phe TTT 5 8 3 3 6 | Ser TCT 4 2 6 7 6 | Tyr TAT 3 2 3 1 1 | Cys TGT 2 1 1 2 2 TTC 10 9 13 11 8 | TCC 6 7 7 3 8 | TAC 3 3 3 5 5 | TGC 1 1 1 3 3 Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 TTG 0 2 1 4 5 | TCG 0 1 0 0 2 | TAG 0 0 0 0 0 | Trp TGG 3 3 3 3 4 -------------------------------------------------------------------------------------------------- Leu CTT 1 1 0 1 3 | Pro CCT 7 2 4 7 3 | His CAT 2 4 4 5 6 | Arg CGT 1 2 1 2 1 CTC 5 4 4 4 7 | CCC 3 6 5 4 7 | CAC 16 11 15 14 12 | CGC 0 1 0 0 0 CTA 1 2 0 2 1 | CCA 2 0 1 0 0 | Gln CAA 0 0 0 0 1 | CGA 0 0 0 0 0 CTG 29 28 30 21 15 | CCG 2 2 1 0 0 | CAG 4 4 5 5 7 | CGG 1 0 1 0 0 -------------------------------------------------------------------------------------------------- Ile ATT 0 0 1 4 1 | Thr ACT 3 4 4 3 10 | Asn AAT 1 5 5 3 2 | Ser AGT 2 3 5 2 1 ATC 0 0 3 2 7 | ACC 12 11 12 9 9 | AAC 9 7 7 8 4 | AGC 4 4 3 5 3 ATA 0 0 0 1 0 | ACA 1 0 0 1 0 | Lys AAA 4 3 5 5 3 | Arg AGA 0 1 0 0 2 Met ATG 3 3 2 4 5 | ACG 0 0 0 0 0 | AAG 18 21 19 19 21 | AGG 4 3 4 4 2 -------------------------------------------------------------------------------------------------- Val GTT 5 5 4 4 6 | Ala GCT 8 11 8 13 10 | Asp GAT 5 8 1 11 6 | Gly GGT 5 4 5 6 10 GTC 4 6 2 4 3 | GCC 21 18 16 18 19 | GAC 10 10 10 8 10 | GGC 14 15 14 12 5 GTA 0 0 0 1 1 | GCA 0 1 1 3 2 | Glu GAA 2 2 7 4 4 | GGA 0 1 0 3 3 GTG 21 19 21 14 14 | GCG 7 4 3 0 0 | GAG 10 9 10 5 6 | GGG 1 1 1 2 2 -------------------------------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: human position 1: T:0.12982 C:0.25965 A:0.21404 G:0.39649 position 2: T:0.29474 C:0.26667 A:0.30526 G:0.13333 position 3: T:0.18947 C:0.41404 A:0.03509 G:0.36140 #2: goat-cow position 1: T:0.13684 C:0.23509 A:0.22807 G:0.40000 position 2: T:0.30526 C:0.24211 A:0.31228 G:0.14035 position 3: T:0.21754 C:0.39649 A:0.03509 G:0.35088 #3: rabbit position 1: T:0.14386 C:0.24912 A:0.24561 G:0.36140 position 2: T:0.29474 C:0.23860 A:0.32982 G:0.13684 position 3: T:0.19298 C:0.40351 A:0.04912 G:0.35439 #4: rat position 1: T:0.14737 C:0.22807 A:0.24561 G:0.37895 position 2: T:0.28070 C:0.23860 A:0.32632 G:0.15439 position 3: T:0.25965 C:0.38596 A:0.07018 G:0.28421 #5: marsupial position 1: T:0.17895 C:0.22105 A:0.24561 G:0.35439 position 2: T:0.28772 C:0.27018 A:0.30877 G:0.13333 position 3: T:0.25965 C:0.38596 A:0.06316 G:0.29123 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 25 | Ser S TCT 25 | Tyr Y TAT 10 | Cys C TGT 8 TTC 51 | TCC 31 | TAC 19 | TGC 9 Leu L TTA 0 | TCA 1 | *** * TAA 0 | *** * TGA 0 TTG 12 | TCG 3 | TAG 0 | Trp W TGG 16 ------------------------------------------------------------------------------ Leu L CTT 6 | Pro P CCT 23 | His H CAT 21 | Arg R CGT 7 CTC 24 | CCC 25 | CAC 68 | CGC 1 CTA 6 | CCA 3 | Gln Q CAA 1 | CGA 0 CTG 123 | CCG 5 | CAG 25 | CGG 2 ------------------------------------------------------------------------------ Ile I ATT 6 | Thr T ACT 24 | Asn N AAT 16 | Ser S AGT 13 ATC 12 | ACC 53 | AAC 35 | AGC 19 ATA 1 | ACA 2 | Lys K AAA 20 | Arg R AGA 3 Met M ATG 17 | ACG 0 | AAG 98 | AGG 17 ------------------------------------------------------------------------------ Val V GTT 24 | Ala A GCT 50 | Asp D GAT 31 | Gly G GGT 30 GTC 19 | GCC 92 | GAC 48 | GGC 60 GTA 2 | GCA 7 | Glu E GAA 19 | GGA 7 GTG 89 | GCG 14 | GAG 40 | GGG 7 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.14737 C:0.23860 A:0.23579 G:0.37825 position 2: T:0.29263 C:0.25123 A:0.31649 G:0.13965 position 3: T:0.22386 C:0.39719 A:0.05053 G:0.32842 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) human goat-cow 0.2507 (0.0863 0.3443) rabbit 0.2627 (0.0867 0.3301) 0.2943 (0.1054 0.3581) rat 0.2045 (0.1261 0.6164) 0.2462 (0.1493 0.6065) 0.2178 (0.1348 0.6187) marsupial 0.1902 (0.1931 1.0148) 0.1891 (0.1910 1.0099) 0.2184 (0.2111 0.9668) 0.2716 (0.2404 0.8852) pairwise comparison, codon frequencies: F3x4. 2 (goat-cow) ... 1 (human) lnL =-1508.607268 0.47825 2.29137 0.19479 t= 0.4783 S= 186.0 N= 669.0 dN/dS= 0.1948 dN= 0.0839 dS= 0.4309 3 (rabbit) ... 1 (human) lnL =-1512.583367 0.46755 2.19039 0.19819 t= 0.4676 S= 179.9 N= 675.1 dN/dS= 0.1982 dN= 0.0842 dS= 0.4247 3 (rabbit) ... 2 (goat-cow) lnL =-1557.337680 0.53837 2.26427 0.22670 t= 0.5384 S= 183.5 N= 671.5 dN/dS= 0.2267 dN= 0.1036 dS= 0.4570 4 (rat) ... 1 (human) lnL =-1649.727994 0.82576 1.78920 0.15108 t= 0.8258 S= 190.2 N= 664.8 dN/dS= 0.1511 dN= 0.1223 dS= 0.8097 4 (rat) ... 2 (goat-cow) lnL =-1677.101606 0.88091 2.40576 0.18757 t= 0.8809 S= 200.2 N= 654.8 dN/dS= 0.1876 dN= 0.1458 dS= 0.7773 4 (rat) ... 3 (rabbit) lnL =-1666.440696 0.85281 2.21652 0.16114 t= 0.8528 S= 193.2 N= 661.8 dN/dS= 0.1611 dN= 0.1306 dS= 0.8105 5 (marsupial) ... 1 (human) lnL =-1769.079306 2.29076 0.98664 0.05689 t= 2.2908 S= 176.2 N= 678.8 dN/dS= 0.0569 dN= 0.1729 dS= 3.0396 5 (marsupial) ... 2 (goat-cow) lnL =-1774.766235 1.80490 1.19637 0.08052 t= 1.8049 S= 180.8 N= 674.2 dN/dS= 0.0805 dN= 0.1762 dS= 2.1879 5 (marsupial) ... 3 (rabbit) lnL =-1794.595175 2.09985 1.06589 0.06930 t= 2.0998 S= 173.1 N= 681.9 dN/dS= 0.0693 dN= 0.1882 dS= 2.7162 5 (marsupial) ... 4 (rat) lnL =-1842.638722 1.66307 1.02118 0.12318 t= 1.6631 S= 180.6 N= 674.4 dN/dS= 0.1232 dN= 0.2214 dS= 1.7973 Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml315.mlc0000644000175000017500000001370013316145226021522 0ustar carandraugcarandraugCODONML (in paml 3.15, November 2005) /tmp/I7ZhE4PgvE/V8dSv7iz0l Model: One dN/dS ratio Codon frequencies: F3x4 ns = 4 ls = 573 Codon usage in sequences -------------------------------------------------------------------------------------- Phe TTT 4 4 5 3 | Ser TCT 16 15 11 15 | Tyr TAT 11 11 14 14 | Cys TGT 2 1 2 1 TTC 7 7 8 8 | TCC 12 8 16 8 | TAC 14 14 10 11 | TGC 1 2 1 2 Leu TTA 1 1 1 2 | TCA 5 7 3 6 | *** TAA 0 0 0 0 | *** TGA 0 0 0 0 TTG 5 5 8 7 | TCG 5 5 8 6 | TAG 0 0 0 0 | Trp TGG 6 6 6 6 -------------------------------------------------------------------------------------- Leu CTT 7 7 10 8 | Pro CCT 22 21 18 17 | His CAT 5 3 3 5 | Arg CGT 3 2 2 2 CTC 14 15 13 17 | CCC 11 13 12 16 | CAC 4 3 5 5 | CGC 4 5 5 4 CTA 1 1 0 2 | CCA 12 13 14 11 | Gln CAA 38 38 40 38 | CGA 4 3 4 2 CTG 7 7 4 4 | CCG 14 13 12 13 | CAG 33 34 28 31 | CGG 2 3 4 5 -------------------------------------------------------------------------------------- Ile ATT 3 4 4 3 | Thr ACT 6 8 4 5 | Asn AAT 9 10 9 6 | Ser AGT 3 3 5 3 ATC 11 11 9 10 | ACC 5 4 7 7 | AAC 14 13 12 15 | AGC 4 4 5 6 ATA 1 2 2 2 | ACA 4 3 9 8 | Lys AAA 6 7 5 4 | Arg AGA 6 7 7 7 Met ATG 9 9 11 8 | ACG 10 9 5 5 | AAG 16 15 17 19 | AGG 7 7 4 5 -------------------------------------------------------------------------------------- Val GTT 3 4 5 5 | Ala GCT 16 16 16 18 | Asp GAT 14 14 15 18 | Gly GGT 17 16 17 18 GTC 8 8 8 8 | GCC 19 18 15 18 | GAC 13 15 13 10 | GGC 8 9 10 9 GTA 7 6 7 6 | GCA 16 17 11 14 | Glu GAA 16 17 19 15 | GGA 7 7 4 6 GTG 5 7 6 7 | GCG 10 8 18 10 | GAG 24 22 21 23 | GGG 6 6 6 6 -------------------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: R265 position 1: T:0.15532 C:0.31588 A:0.19895 G:0.32984 position 2: T:0.16230 C:0.31937 A:0.37871 G:0.13962 position 3: T:0.24607 C:0.26003 A:0.21640 G:0.27749 #2: WM276 position 1: T:0.15009 C:0.31588 A:0.20244 G:0.33159 position 2: T:0.17103 C:0.31065 A:0.37696 G:0.14136 position 3: T:0.24258 C:0.26003 A:0.22513 G:0.27225 #3: H99 position 1: T:0.16230 C:0.30366 A:0.20070 G:0.33333 position 2: T:0.17627 C:0.31239 A:0.36824 G:0.14311 position 3: T:0.24433 C:0.26003 A:0.21990 G:0.27574 #4: JEC21 position 1: T:0.15532 C:0.31414 A:0.19721 G:0.33333 position 2: T:0.17452 C:0.30890 A:0.37347 G:0.14311 position 3: T:0.24607 C:0.26876 A:0.21466 G:0.27051 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 16 | Ser S TCT 57 | Tyr Y TAT 50 | Cys C TGT 6 TTC 30 | TCC 44 | TAC 49 | TGC 6 Leu L TTA 5 | TCA 21 | *** * TAA 0 | *** * TGA 0 TTG 25 | TCG 24 | TAG 0 | Trp W TGG 24 ------------------------------------------------------------------------------ Leu L CTT 32 | Pro P CCT 78 | His H CAT 16 | Arg R CGT 9 CTC 59 | CCC 52 | CAC 17 | CGC 18 CTA 4 | CCA 50 | Gln Q CAA 154 | CGA 13 CTG 22 | CCG 52 | CAG 126 | CGG 14 ------------------------------------------------------------------------------ Ile I ATT 14 | Thr T ACT 23 | Asn N AAT 34 | Ser S AGT 14 ATC 41 | ACC 23 | AAC 54 | AGC 19 ATA 7 | ACA 24 | Lys K AAA 22 | Arg R AGA 27 Met M ATG 37 | ACG 29 | AAG 67 | AGG 23 ------------------------------------------------------------------------------ Val V GTT 17 | Ala A GCT 66 | Asp D GAT 61 | Gly G GGT 68 GTC 32 | GCC 70 | GAC 51 | GGC 36 GTA 26 | GCA 58 | Glu E GAA 67 | GGA 24 GTG 25 | GCG 46 | GAG 90 | GGG 24 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.15576 C:0.31239 A:0.19983 G:0.33202 position 2: T:0.17103 C:0.31283 A:0.37435 G:0.14180 position 3: T:0.24476 C:0.26222 A:0.21902 G:0.27400 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) R265 WM276 0.2264 (0.0186 0.0821) H99 0.1481 (0.0586 0.3959) 0.1481 (0.0611 0.4126) JEC21 0.1112 (0.0421 0.3787) 0.1173 (0.0466 0.3970) 0.1419 (0.0380 0.2679) pairwise comparison, codon frequencies: F3x4. 2 (WM276) ... 1 (R265) lnL =-2569.912690 0.10404 3.29148 0.32693 t= 0.1040 S= 541.4 N= 1177.6 dN/dS= 0.3269 dN= 0.0210 dS= 0.0644 3 (H99) ... 1 (R265) lnL =-3019.970151 0.43604 3.31017 0.20554 t= 0.4360 S= 540.2 N= 1178.8 dN/dS= 0.2055 dN= 0.0656 dS= 0.3193 3 (H99) ... 2 (WM276) lnL =-3036.174074 0.45547 3.63495 0.20989 t= 0.4555 S= 547.4 N= 1171.6 dN/dS= 0.2099 dN= 0.0691 dS= 0.3290 4 (JEC21) ... 1 (R265) lnL =-2937.357570 0.38462 2.95077 0.15134 t= 0.3846 S= 530.2 N= 1188.8 dN/dS= 0.1513 dN= 0.0470 dS= 0.3104 4 (JEC21) ... 2 (WM276) lnL =-2966.384266 0.41002 3.25414 0.16413 t= 0.4100 S= 538.1 N= 1180.9 dN/dS= 0.1641 dN= 0.0527 dS= 0.3210 4 (JEC21) ... 3 (H99) lnL =-2844.283241 0.29120 4.67661 0.21504 t= 0.2912 S= 566.5 N= 1152.5 dN/dS= 0.2150 dN= 0.0441 dS= 0.2049 Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml_nan.mlc0000644000175000017500000002443113316145226022130 0ustar carandraugcarandraug seed used = 785596301 Data set 1 3 141 all_s57600 CTC TTC CAC ACC TCC CAC TCC CCC CCC CTC CAC TCC TTC TTC ACC TCC CCT TCC CCC TCC CTC CTT CCC TCC CCC ACC CTC TTC CTT TTC CCC TTC CAC TCC CCC TTC CTC CGC CTC CCC TCC CTC CCC CCC CAC CAC CCC all_s56012 CTC CTC CTC ACC TCC CAC TCC CCC CCC TTC CAC TCC TTC TTC ACC CCC CCC TCC CCC CCC CTC CTC CCC TCC CCC ACC CTC TTC CTC TTC CCC TTC CAC TCC TCC TTC CTC CGC CTC TCC TCC CTC CCC CCC CAC CAC CCC all_c11513 CTC CTC CTC ACC TCC CAC TCC CCC CCC TTC CAC TCC TTC TTC ACC CCC CCC TCC CCC CCC CTC CTC CCC TCC CCC ACC CCC TTC CTC TTC CCC TTC CAC TCC TCC TTC CTC CGC CTC TCC TCC CTC CCC CCC CAC CAC CCC Printing out site pattern counts 11 93 P all_s57600 ACC CAC CAC CAC CAC CCC CCC CCC CCC CCC CCC CCT CGC CTC CTC CTC CTC CTC CTC CTT CTT TCC TCC TCC TCC TCC TCC TCC TTC TTC TTC all_s56012 ... ... ... ... .T. ... ... ... ... ... T.. ..C ... ... ... ... ... ... T.. ..C ..C C.. C.. ... ... ... ... ... C.. ... ... all_c11513 ... ... ... ... .T. ... ... ... ... ... T.. ..C ... .C. ... ... ... ... T.. ..C ..C C.. C.. ... ... ... ... ... C.. ... ... 3 3 1 1 1 1 5 1 1 1 2 1 1 1 1 2 1 1 1 1 1 1 1 1 1 3 1 1 1 5 1 CODONML (in paml version 4.4, January 2010) /scratch/davepaml17/cluster45_fake.phy Model: One dN/dS ratio for branches Global clock Codon frequency model: F3x4 ns = 3 ls = 47 Codon usage in sequences -------------------------------------------------------------------------------------------------------------- Phe TTT 0 0 0 1 0 0 | Ser TCT 0 0 0 0 0 0 | Tyr TAT 0 0 0 0 0 0 | Cys TGT 0 0 0 0 0 0 TTC 7 7 7 7 9 7 | TCC 9 10 8 10 8 9 | TAC 0 0 0 0 0 0 | TGC 0 0 0 0 0 0 Leu TTA 0 0 0 0 0 0 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 TTG 0 0 0 0 0 0 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------- Leu CTT 2 1 1 2 1 0 | Pro CCT 1 0 0 0 0 0 | His CAT 0 0 0 0 0 0 | Arg CGT 0 0 0 0 1 0 CTC 7 9 4 6 8 10 | CCC 11 11 19 12 13 12 | CAC 6 5 4 5 4 5 | CGC 1 1 1 0 0 1 CTA 0 0 0 0 0 0 | CCA 0 0 0 0 0 0 | Gln CAA 0 0 0 0 0 0 | CGA 0 0 0 0 0 0 CTG 0 0 0 0 0 0 | CCG 0 0 0 0 0 0 | CAG 0 0 0 0 0 0 | CGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------- Ile ATT 0 0 0 0 0 0 | Thr ACT 0 0 0 0 0 0 | Asn AAT 0 0 0 0 0 0 | Ser AGT 0 0 0 0 0 0 ATC 0 0 0 0 0 0 | ACC 3 3 3 4 3 3 | AAC 0 0 0 0 0 0 | AGC 0 0 0 0 0 0 ATA 0 0 0 0 0 0 | ACA 0 0 0 0 0 0 | Lys AAA 0 0 0 0 0 0 | Arg AGA 0 0 0 0 0 0 Met ATG 0 0 0 0 0 0 | ACG 0 0 0 0 0 0 | AAG 0 0 0 0 0 0 | AGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------- Val GTT 0 0 0 0 0 0 | Ala GCT 0 0 0 0 0 0 | Asp GAT 0 0 0 0 0 0 | Gly GGT 0 0 0 0 0 0 GTC 0 0 0 0 0 0 | GCC 0 0 0 0 0 0 | GAC 0 0 0 0 0 0 | GGC 0 0 0 0 0 0 GTA 0 0 0 0 0 0 | GCA 0 0 0 0 0 0 | Glu GAA 0 0 0 0 0 0 | GGA 0 0 0 0 0 0 GTG 0 0 0 0 0 0 | GCG 0 0 0 0 0 0 | GAG 0 0 0 0 0 0 | GGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------------------- Phe TTT 0 0 0 0 0 | Ser TCT 0 0 0 0 0 | Tyr TAT 0 0 0 0 0 | Cys TGT 0 0 0 0 0 TTC 7 8 9 7 7 | TCC 9 12 9 10 10 | TAC 0 0 0 0 0 | TGC 0 0 0 0 0 Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 0 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 TTG 0 0 0 0 0 | TCG 0 0 0 0 0 | TAG 0 0 0 0 0 | Trp TGG 0 0 0 0 0 -------------------------------------------------------------------------------------------------- Leu CTT 0 1 1 1 1 | Pro CCT 0 0 1 0 0 | His CAT 0 0 1 0 0 | Arg CGT 0 0 0 0 0 CTC 9 8 6 9 9 | CCC 13 8 11 11 11 | CAC 5 5 5 5 5 | CGC 1 1 0 1 1 CTA 0 0 0 0 0 | CCA 0 0 0 0 0 | Gln CAA 0 0 0 0 0 | CGA 0 0 0 0 0 CTG 0 0 0 0 0 | CCG 0 0 0 0 0 | CAG 0 0 0 0 0 | CGG 0 0 0 0 0 -------------------------------------------------------------------------------------------------- Ile ATT 0 0 0 0 0 | Thr ACT 0 0 0 0 0 | Asn AAT 0 0 0 0 0 | Ser AGT 0 0 0 0 0 ATC 0 0 0 0 0 | ACC 3 4 4 3 3 | AAC 0 0 0 0 0 | AGC 0 0 0 0 0 ATA 0 0 0 0 0 | ACA 0 0 0 0 0 | Lys AAA 0 0 0 0 0 | Arg AGA 0 0 0 0 0 Met ATG 0 0 0 0 0 | ACG 0 0 0 0 0 | AAG 0 0 0 0 0 | AGG 0 0 0 0 0 -------------------------------------------------------------------------------------------------- Val GTT 0 0 0 0 0 | Ala GCT 0 0 0 0 0 | Asp GAT 0 0 0 0 0 | Gly GGT 0 0 0 0 0 GTC 0 0 0 0 0 | GCC 0 0 0 0 0 | GAC 0 0 0 0 0 | GGC 0 0 0 0 0 GTA 0 0 0 0 0 | GCA 0 0 0 0 0 | Glu GAA 0 0 0 0 0 | GGA 0 0 0 0 0 GTG 0 0 0 0 0 | GCG 0 0 0 0 0 | GAG 0 0 0 0 0 | GGG 0 0 0 0 0 -------------------------------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: all_s57600 position 1: T:0.34043 C:0.59574 A:0.06383 G:0.00000 position 2: T:0.34043 C:0.51064 A:0.12766 G:0.02128 position 3: T:0.06383 C:0.93617 A:0.00000 G:0.00000 Average T:0.24823 C:0.68085 A:0.06383 G:0.00709 #2: all_s56012 position 1: T:0.34043 C:0.59574 A:0.06383 G:0.00000 position 2: T:0.36170 C:0.51064 A:0.10638 G:0.02128 position 3: T:0.00000 C:1.00000 A:0.00000 G:0.00000 Average T:0.23404 C:0.70213 A:0.05674 G:0.00709 #3: all_c11513 position 1: T:0.34043 C:0.59574 A:0.06383 G:0.00000 position 2: T:0.34043 C:0.53191 A:0.10638 G:0.02128 position 3: T:0.00000 C:1.00000 A:0.00000 G:0.00000 Average T:0.22695 C:0.70922 A:0.05674 G:0.00709 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 1 | Ser S TCT 0 | Tyr Y TAT 0 | Cys C TGT 0 TTC 82 | TCC 104 | TAC 0 | TGC 0 Leu L TTA 0 | TCA 0 | *** * TAA 0 | *** * TGA 0 TTG 0 | TCG 0 | TAG 0 | Trp W TGG 0 ------------------------------------------------------------------------------ Leu L CTT 11 | Pro P CCT 2 | His H CAT 1 | Arg R CGT 1 CTC 85 | CCC 132 | CAC 54 | CGC 8 CTA 0 | CCA 0 | Gln Q CAA 0 | CGA 0 CTG 0 | CCG 0 | CAG 0 | CGG 0 ------------------------------------------------------------------------------ Ile I ATT 0 | Thr T ACT 0 | Asn N AAT 0 | Ser S AGT 0 ATC 0 | ACC 36 | AAC 0 | AGC 0 ATA 0 | ACA 0 | Lys K AAA 0 | Arg R AGA 0 Met M ATG 0 | ACG 0 | AAG 0 | AGG 0 ------------------------------------------------------------------------------ Val V GTT 0 | Ala A GCT 0 | Asp D GAT 0 | Gly G GGT 0 GTC 0 | GCC 0 | GAC 0 | GGC 0 GTA 0 | GCA 0 | Glu E GAA 0 | GGA 0 GTG 0 | GCG 0 | GAG 0 | GGG 0 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.36170 C:0.56867 A:0.06963 G:0.00000 position 2: T:0.34623 C:0.52998 A:0.10638 G:0.01741 position 3: T:0.03095 C:0.96905 A:0.00000 G:0.00000 Average T:0.24629 C:0.68923 A:0.05867 G:0.00580 Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): 0.00387564 0.12135585 0.00000000 0.00000000 0.00593254 0.18576259 0.00000000 0.00000000 0.00119084 0.03728811 0.00000000 0.00000000 0.00019486 0.00610169 0.00000000 0.00000000 0.00609325 0.19079477 0.00000000 0.00000000 0.00932709 0.29205456 0.00000000 0.00000000 0.00187223 0.05862409 0.00000000 0.00000000 0.00030636 0.00959303 0.00000000 0.00000000 0.00074611 0.02336262 0.00000000 0.00000000 0.00114209 0.03576178 0.00000000 0.00000000 0.00022925 0.00717846 0.00000000 0.00000000 0.00003751 0.00117466 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later ML. analysis. Use runmode = -2 for ML pairwise comparison.) all_s57600 all_s56012 0.8758 (0.0717 0.0819) all_c11513 1.0080 (0.0826 0.0819) 0.7616 (0.0199 0.0261) pairwise comparison, codon frequencies: F3x4. 2 (all_c56012) ... 1 (all_s57600) lnL = -126.880601 0.19045 2.92330 0.10941 t= 0.1904 S= 5.8 N= 135.2 dN/dS= 0.1094 dN= 0.0476 dS= 0.4353 3 (all_c11513) ... 1 (all_c57600) lnL = -142.636697 4.21113 0.72684 0.00175 t= 4.2111 S= 4.2 N= 136.8 dN/dS= 0.0018 dN= 0.0789 dS=44.9635 3 (all_c11513) ... 2 (all_s56012) lnL = -93.410530 0.02176 999.00000 0.13702 t= 0.0218 S= 0.0 N= 141.0 dN/dS= 0.1370 dN= 0.0073 dS= nan Bio-Tools-Phylo-PAML-1.7.3/t/data/yn00.mlc0000644000175000017500000001341513316145226020617 0ustar carandraugcarandraugYN00 examples/abglobin.nuc ns = 5 ls = 285 Codon position x base (3x4) table for each sequence. human position 1: T:0.12982 C:0.25965 A:0.21404 G:0.39649 position 2: T:0.29474 C:0.26667 A:0.30526 G:0.13333 position 3: T:0.18947 C:0.41404 A:0.03509 G:0.36140 goat-cow position 1: T:0.13684 C:0.23509 A:0.22807 G:0.40000 position 2: T:0.30526 C:0.24211 A:0.31228 G:0.14035 position 3: T:0.21754 C:0.39649 A:0.03509 G:0.35088 rabbit position 1: T:0.14386 C:0.24912 A:0.24561 G:0.36140 position 2: T:0.29474 C:0.23860 A:0.32982 G:0.13684 position 3: T:0.19298 C:0.40351 A:0.04912 G:0.35439 rat position 1: T:0.14737 C:0.22807 A:0.24561 G:0.37895 position 2: T:0.28070 C:0.23860 A:0.32632 G:0.15439 position 3: T:0.25965 C:0.38596 A:0.07018 G:0.28421 marsupial position 1: T:0.17895 C:0.22105 A:0.24561 G:0.35439 position 2: T:0.28772 C:0.27018 A:0.30877 G:0.13333 position 3: T:0.25965 C:0.38596 A:0.06316 G:0.29123 Average position 1: T:0.14737 C:0.23860 A:0.23579 G:0.37825 position 2: T:0.29263 C:0.25123 A:0.31649 G:0.13965 position 3: T:0.22386 C:0.39719 A:0.05053 G:0.32842 Codon usage for each species -------------------------------------------------------------------------------------------------- Phe TTT 5 8 3 3 6 | Ser TCT 4 2 6 7 6 | Tyr TAT 3 2 3 1 1 | Cys TGT 2 1 1 2 2 TTC 10 9 13 11 8 | TCC 6 7 7 3 8 | TAC 3 3 3 5 5 | TGC 1 1 1 3 3 Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 TTG 0 2 1 4 5 | TCG 0 1 0 0 2 | TAG 0 0 0 0 0 | Trp TGG 3 3 3 3 4 -------------------------------------------------------------------------------------------------- Leu CTT 1 1 0 1 3 | Pro CCT 7 2 4 7 3 | His CAT 2 4 4 5 6 | Arg CGT 1 2 1 2 1 CTC 5 4 4 4 7 | CCC 3 6 5 4 7 | CAC 16 11 15 14 12 | CGC 0 1 0 0 0 CTA 1 2 0 2 1 | CCA 2 0 1 0 0 | Gln CAA 0 0 0 0 1 | CGA 0 0 0 0 0 CTG 29 28 30 21 15 | CCG 2 2 1 0 0 | CAG 4 4 5 5 7 | CGG 1 0 1 0 0 -------------------------------------------------------------------------------------------------- Ile ATT 0 0 1 4 1 | Thr ACT 3 4 4 3 10 | Asn AAT 1 5 5 3 2 | Ser AGT 2 3 5 2 1 ATC 0 0 3 2 7 | ACC 12 11 12 9 9 | AAC 9 7 7 8 4 | AGC 4 4 3 5 3 ATA 0 0 0 1 0 | ACA 1 0 0 1 0 | Lys AAA 4 3 5 5 3 | Arg AGA 0 1 0 0 2 Met ATG 3 3 2 4 5 | ACG 0 0 0 0 0 | AAG 18 21 19 19 21 | AGG 4 3 4 4 2 -------------------------------------------------------------------------------------------------- Val GTT 5 5 4 4 6 | Ala GCT 8 11 8 13 10 | Asp GAT 5 8 1 11 6 | Gly GGT 5 4 5 6 10 GTC 4 6 2 4 3 | GCC 21 18 16 18 19 | GAC 10 10 10 8 10 | GGC 14 15 14 12 5 GTA 0 0 0 1 1 | GCA 0 1 1 3 2 | Glu GAA 2 2 7 4 4 | GGA 0 1 0 3 3 GTG 21 19 21 14 14 | GCG 7 4 3 0 0 | GAG 10 9 10 5 6 | GGG 1 1 1 2 2 -------------------------------------------------------------------------------------------------- Sums -------------------------------------------------- Phe TTT 25 | Ser TCT 25 | Tyr TAT 10 | Cys TGT 8 TTC 51 | TCC 31 | TAC 19 | TGC 9 Leu TTA 0 | TCA 1 | *** TAA 0 | *** TGA 0 TTG 12 | TCG 3 | TAG 0 | Trp TGG 16 -------------------------------------------------- Leu CTT 6 | Pro CCT 23 | His CAT 21 | Arg CGT 7 CTC 24 | CCC 25 | CAC 68 | CGC 1 CTA 6 | CCA 3 | Gln CAA 1 | CGA 0 CTG 123 | CCG 5 | CAG 25 | CGG 2 -------------------------------------------------- Ile ATT 6 | Thr ACT 24 | Asn AAT 16 | Ser AGT 13 ATC 12 | ACC 53 | AAC 35 | AGC 19 ATA 1 | ACA 2 | Lys AAA 20 | Arg AGA 3 Met ATG 17 | ACG 0 | AAG 98 | AGG 17 -------------------------------------------------- Val GTT 24 | Ala GCT 50 | Asp GAT 31 | Gly GGT 30 GTC 19 | GCC 92 | GAC 48 | GGC 60 GTA 2 | GCA 7 | Glu GAA 19 | GGA 7 GTG 89 | GCG 14 | GAG 40 | GGG 7 -------------------------------------------------- Nei & Gojobori 1986. dN/dS (dN, dS) human goat-cow 0.251(0.0863 0.3443) rabbit 0.263(0.0867 0.3301) 0.294(0.1054 0.3581) rat 0.204(0.1261 0.6164) 0.246(0.1493 0.6065) 0.218(0.1348 0.6187) marsupial 0.190(0.1931 1.0148) 0.189(0.1910 1.0099) 0.218(0.2111 0.9668) 0.272(0.2404 0.8852) Estimation by the method of Yang & Nielsen (2000): (equal weighting of pathways) seq. seq. S N t kappa omega dN +- SE dS +- SE 2 1 183.7 671.3 0.5169 1.5804 0.1625 0.0818 +- 0.0115 0.5031 +- 0.0930 3 1 177.5 677.5 0.5033 1.5804 0.1642 0.0815 +- 0.0114 0.4967 +- 0.0927 3 2 180.1 674.9 0.5627 1.5804 0.1929 0.0997 +- 0.0128 0.5169 +- 0.0925 4 1 191.3 663.7 0.9075 1.5804 0.1308 0.1216 +- 0.0144 0.9301 +- 0.1987 4 2 192.4 662.6 0.9642 1.5804 0.1557 0.1447 +- 0.0159 0.9297 +- 0.2091 4 3 187.0 668.0 0.9790 1.5804 0.1262 0.1298 +- 0.0149 1.0286 +- 0.2614 5 1 189.3 665.7 2.1638 1.5804 0.0711 0.1853 +- 0.0184 2.6055 +- 3.9344 5 2 190.4 664.6 1.2984 1.5804 0.1416 0.1842 +- 0.0184 1.3008 +- 0.1995 5 3 185.2 669.8 1.3214 1.5804 0.1554 0.2023 +- 0.0194 1.3020 +- 0.2026 5 4 194.5 660.5 1.5554 1.5804 0.1591 0.2354 +- 0.0215 1.4797 +- 0.5173 Bio-Tools-Phylo-PAML-1.7.3/t/data/M0.mlc0000644000175000017500000001460213316145226020304 0ustar carandraugcarandraugCODONML (in paml 3.15, November 2005) test.phy Model: One dN/dS ratio Codon frequencies: F3x4 Site-class models: ns = 3 ls = 6 Codon usage in sequences -------------------------------------------------------------------------- Phe TTT 1 1 1 | Ser TCT 1 1 0 | Tyr TAT 0 0 0 | Cys TGT 0 0 0 TTC 0 0 0 | TCC 0 0 1 | TAC 0 0 0 | TGC 0 0 0 Leu TTA 0 0 0 | TCA 0 0 0 | *** TAA 0 0 0 | *** TGA 0 0 0 TTG 0 0 0 | TCG 0 0 0 | TAG 0 0 0 | Trp TGG 0 0 0 -------------------------------------------------------------------------- Leu CTT 0 0 0 | Pro CCT 0 0 0 | His CAT 1 1 1 | Arg CGT 0 0 0 CTC 0 0 0 | CCC 0 0 1 | CAC 0 0 0 | CGC 0 0 0 CTA 0 0 0 | CCA 1 1 0 | Gln CAA 0 0 0 | CGA 0 0 0 CTG 0 0 0 | CCG 0 0 0 | CAG 0 0 0 | CGG 0 0 0 -------------------------------------------------------------------------- Ile ATT 0 0 0 | Thr ACT 0 0 0 | Asn AAT 0 0 0 | Ser AGT 0 0 0 ATC 0 0 0 | ACC 0 0 0 | AAC 0 0 0 | AGC 0 0 0 ATA 0 0 0 | ACA 0 0 0 | Lys AAA 0 0 0 | Arg AGA 0 0 0 Met ATG 2 1 1 | ACG 0 1 1 | AAG 0 0 0 | AGG 0 0 0 -------------------------------------------------------------------------- Val GTT 0 0 0 | Ala GCT 0 0 0 | Asp GAT 0 0 0 | Gly GGT 0 0 0 GTC 0 0 0 | GCC 0 0 0 | GAC 0 0 0 | GGC 0 0 0 GTA 0 0 0 | GCA 0 0 0 | Glu GAA 0 0 0 | GGA 0 0 0 GTG 0 0 0 | GCG 0 0 0 | GAG 0 0 0 | GGG 0 0 0 -------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: test0 position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 position 2: T:0.50000 C:0.33333 A:0.16667 G:0.00000 position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333 #2: test1 position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000 position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333 #3: test2 position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000 position 3: T:0.33333 C:0.33333 A:0.00000 G:0.33333 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 3 | Ser S TCT 2 | Tyr Y TAT 0 | Cys C TGT 0 TTC 0 | TCC 1 | TAC 0 | TGC 0 Leu L TTA 0 | TCA 0 | *** * TAA 0 | *** * TGA 0 TTG 0 | TCG 0 | TAG 0 | Trp W TGG 0 ------------------------------------------------------------------------------ Leu L CTT 0 | Pro P CCT 0 | His H CAT 3 | Arg R CGT 0 CTC 0 | CCC 1 | CAC 0 | CGC 0 CTA 0 | CCA 2 | Gln Q CAA 0 | CGA 0 CTG 0 | CCG 0 | CAG 0 | CGG 0 ------------------------------------------------------------------------------ Ile I ATT 0 | Thr T ACT 0 | Asn N AAT 0 | Ser S AGT 0 ATC 0 | ACC 0 | AAC 0 | AGC 0 ATA 0 | ACA 0 | Lys K AAA 0 | Arg R AGA 0 Met M ATG 4 | ACG 2 | AAG 0 | AGG 0 ------------------------------------------------------------------------------ Val V GTT 0 | Ala A GCT 0 | Asp D GAT 0 | Gly G GGT 0 GTC 0 | GCC 0 | GAC 0 | GGC 0 GTA 0 | GCA 0 | Glu E GAA 0 | GGA 0 GTG 0 | GCG 0 | GAG 0 | GGG 0 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 position 2: T:0.38889 C:0.44444 A:0.16667 G:0.00000 position 3: T:0.44444 C:0.11111 A:0.11111 G:0.33333 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) test0 test1 -1.0000 (0.0706 0.0000) test2 0.0510 (0.0706 1.3844) 0.0000 (0.0000 0.9745) Model 0: one-ratio TREE # 1: (1, 2, 3); MP score: 3 lnL(ntime: 3 np: 5): -30.819156 +0.000000 4..1 4..2 4..3 0.25573 0.00000 0.62424 5.28487 0.09213 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 0.87997 (1: 0.255727, 2: 0.000004, 3: 0.624239); (test0: 0.255727, test1: 0.000004, test2: 0.624239); Detailed output identifying parameters kappa (ts/tv) = 5.28487 omega (dN/dS) = 0.09213 dN & dS for each branch branch t N S dN/dS dN dS N*dN S*dS 4..1 0.256 12.9 5.1 0.0921 0.0224 0.2429 0.3 1.2 4..2 0.000 12.9 5.1 0.0921 0.0000 0.0000 0.0 0.0 4..3 0.624 12.9 5.1 0.0921 0.0546 0.5930 0.7 3.0 tree length for dN: 0.07702 tree length for dS: 0.83594 Time used: 0:00 Model 1: NearlyNeutral (2 categories) TREE # 1: (1, 2, 3); MP score: 3 lnL(ntime: 3 np: 6): -30.819157 +0.000000 4..1 4..2 4..3 0.25573 0.00000 0.62424 5.28488 1.00000 0.09213 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 0.87997 (1: 0.255727, 2: 0.000004, 3: 0.624240); (test0: 0.255727, test1: 0.000004, test2: 0.624240); Detailed output identifying parameters kappa (ts/tv) = 5.28488 dN/dS for site classes (K=2) p: 1.00000 0.00000 w: 0.09213 1.00000 dN & dS for each branch branch t N S dN/dS dN dS N*dN S*dS 4..1 0.256 12.9 5.1 0.0921 0.0224 0.2429 0.3 1.2 4..2 0.000 12.9 5.1 0.0921 0.0000 0.0000 0.0 0.0 4..3 0.624 12.9 5.1 0.0921 0.0546 0.5930 0.7 3.0 Naive Empirical Bayes (NEB) analysis Time used: 0:02 Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml45b.mlc0000644000175000017500000011035013316145226021603 0ustar carandraugcarandraug 9 1425 Pdel181_DNA2 ATG TCA CCA CAA ACA GAG ACT AAA ACA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAG TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT ACT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATG CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG Pfre186_DNA2 ATG TCA CCA CAA ACA GAG ACT AAA ACA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAG TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT ACT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATG CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT ATT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG Pgra187_DNA2 ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT ACT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG ACT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATG AAA AGG GCT ATA TTT GCC AGA GAA TTG GGA GTT CCT ATT GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCT GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATA AAA TTT GAA TTC GAA GCA ATG GAT ACG TTG Phet26_DNA21 ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTA CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG Pmex37_DNA21 ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT ACT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATG CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT ATT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG Ptre197_DNA2 ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT ACT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG ACT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATG AAA AGG GCT ATA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCT GGT GCT GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC GAA GCA ATG GAT ACG TTG WHR1_DNA225 ATG TCA CCA CAA ACA GAG ACT AAA GCG GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAG TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCC GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT ACT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATG AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG YALD273_DNA5 ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTA CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG Pop_trich_ch ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTA CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG Printing out site pattern counts 9 225 P Pdel181_DNA2 AAA AAC AAG AAT ACA ACA ACC ACG ACT ACT AGA AGC AGG AGT ATA ATC ATC ATC ATG ATG ATT ATT CAA CAA CAC CAG CAT CCA CCC CCC CCG CCT CCT CGA CGC CGT CTA CTG CTG CTT GAA GAC GAG GAG GAT GCA GCC GCC GCT GCT GGA GGC GGG GGT GTA GTA GTC GTG GTT GTT GTT TAC TAT TCA TCC TCG TCT TCT TGC TGG TGT TTA TTC TTG TTT Pfre186_DNA2 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... Pgra187_DNA2 ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ..G ..T ..A ... ..A ... ... G.. ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... A.. ... ... ... ... ... A.. ... ... ... ... AC. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... Phet26_DNA21 ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... Pmex37_DNA21 ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... Ptre197_DNA2 ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ..G ... ..A ... ... ... ... G.. ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ..T A.. ... ... ... ... ... A.. ... ... ... ... AC. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... WHR1_DNA225 ... ... ... ... ... G.G ... ... ... .G. ... ... ... ... ... ... ..G ... ..A ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... YALD273_DNA5 ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... Pop_trich_ch ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 18 6 6 9 5 1 8 1 16 1 6 3 1 1 1 7 1 1 1 9 1 9 9 1 5 2 9 3 5 1 2 1 10 6 5 11 9 1 3 9 24 5 1 9 22 15 4 1 1 23 13 2 9 23 1 12 1 4 1 1 13 4 13 1 4 1 1 5 3 8 5 9 8 10 14 CODONML (in paml version 4.5, December 2011) examples/small_taxon_set.nuc Model: One dN/dS ratio for branches Codon frequency model: F3x4 ns = 9 ls = 475 Codon usage in sequences -------------------------------------------------------------------------------------------------------------- Phe TTT 14 14 14 14 14 14 | Ser TCT 6 6 6 6 6 6 | Tyr TAT 13 13 13 13 13 13 | Cys TGT 5 5 5 5 5 5 TTC 8 8 8 8 8 8 | TCC 4 4 4 4 4 4 | TAC 4 4 4 4 4 4 | TGC 3 3 3 3 3 3 Leu TTA 9 9 9 9 9 9 | TCA 1 1 1 1 1 1 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 TTG 10 10 10 10 10 10 | TCG 1 1 1 1 1 1 | TAG 0 0 0 0 0 0 | Trp TGG 8 8 8 8 8 8 -------------------------------------------------------------------------------------------------------------- Leu CTT 9 9 9 9 9 9 | Pro CCT 11 11 12 11 10 12 | His CAT 9 9 9 9 9 9 | Arg CGT 11 11 11 11 11 11 CTC 0 0 0 0 0 0 | CCC 6 6 5 6 6 5 | CAC 5 5 5 5 5 5 | CGC 5 5 5 5 5 5 CTA 9 9 9 10 9 9 | CCA 3 3 3 3 3 3 | Gln CAA 10 10 9 10 10 9 | CGA 6 6 6 6 6 6 CTG 4 4 4 3 4 4 | CCG 2 2 2 2 2 2 | CAG 2 2 2 2 2 2 | CGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------- Ile ATT 10 11 10 10 11 10 | Thr ACT 17 17 18 16 17 18 | Asn AAT 9 9 9 9 9 9 | Ser AGT 1 1 2 2 2 2 ATC 9 9 7 9 9 8 | ACC 8 8 8 8 8 8 | AAC 6 6 6 6 6 6 | AGC 3 3 3 3 3 3 ATA 1 1 4 2 1 3 | ACA 6 6 5 5 5 5 | Lys AAA 18 18 18 18 18 18 | Arg AGA 6 6 6 6 6 6 Met ATG 10 10 10 9 10 10 | ACG 1 1 1 1 1 1 | AAG 6 6 6 6 6 6 | AGG 1 1 1 1 1 1 -------------------------------------------------------------------------------------------------------------- Val GTT 15 14 14 15 14 14 | Ala GCT 24 24 23 24 24 24 | Asp GAT 22 22 22 22 22 22 | Gly GGT 23 23 23 23 23 23 GTC 1 1 1 1 1 1 | GCC 5 5 5 5 5 4 | GAC 5 5 6 6 6 6 | GGC 2 2 2 2 2 2 GTA 13 13 12 13 13 12 | GCA 15 15 16 16 16 16 | Glu GAA 24 24 25 24 24 25 | GGA 13 13 13 13 13 13 GTG 4 4 4 4 4 4 | GCG 0 0 0 0 0 0 | GAG 10 10 9 9 9 9 | GGG 9 9 9 9 9 9 -------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------- Phe TTT 14 14 14 | Ser TCT 5 6 6 | Tyr TAT 13 13 13 | Cys TGT 5 5 5 TTC 8 8 8 | TCC 5 4 4 | TAC 4 4 4 | TGC 3 3 3 Leu TTA 9 9 9 | TCA 1 1 1 | *** TAA 0 0 0 | *** TGA 0 0 0 TTG 10 10 10 | TCG 1 1 1 | TAG 0 0 0 | Trp TGG 8 8 8 -------------------------------------------------------------------------- Leu CTT 9 9 9 | Pro CCT 10 11 11 | His CAT 9 9 9 | Arg CGT 11 11 11 CTC 0 0 0 | CCC 6 6 6 | CAC 5 5 5 | CGC 5 5 5 CTA 9 10 10 | CCA 3 3 3 | Gln CAA 10 10 10 | CGA 6 6 6 CTG 4 3 3 | CCG 2 2 2 | CAG 2 2 2 | CGG 0 0 0 -------------------------------------------------------------------------- Ile ATT 10 10 10 | Thr ACT 17 16 16 | Asn AAT 9 9 9 | Ser AGT 2 2 2 ATC 8 9 9 | ACC 8 8 8 | AAC 6 6 6 | AGC 3 3 3 ATA 2 2 2 | ACA 5 5 5 | Lys AAA 18 18 18 | Arg AGA 6 6 6 Met ATG 10 9 9 | ACG 1 1 1 | AAG 6 6 6 | AGG 1 1 1 -------------------------------------------------------------------------- Val GTT 15 15 15 | Ala GCT 24 24 24 | Asp GAT 22 22 22 | Gly GGT 23 23 23 GTC 1 1 1 | GCC 5 5 5 | GAC 5 6 6 | GGC 2 2 2 GTA 13 13 13 | GCA 15 16 16 | Glu GAA 24 24 24 | GGA 13 13 13 GTG 4 4 4 | GCG 1 0 0 | GAG 10 9 9 | GGG 9 9 9 -------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: Pdel181_DNA2 position 1: T:0.18105 C:0.19368 A:0.23579 G:0.38947 position 2: T:0.26526 C:0.23158 A:0.30105 G:0.20211 position 3: T:0.41895 C:0.15579 A:0.28211 G:0.14316 Average T:0.28842 C:0.19368 A:0.27298 G:0.24491 #2: Pfre186_DNA2 position 1: T:0.18105 C:0.19368 A:0.23789 G:0.38737 position 2: T:0.26526 C:0.23158 A:0.30105 G:0.20211 position 3: T:0.41895 C:0.15579 A:0.28211 G:0.14316 Average T:0.28842 C:0.19368 A:0.27368 G:0.24421 #3: Pgra187_DNA2 position 1: T:0.18105 C:0.19158 A:0.24000 G:0.38737 position 2: T:0.26316 C:0.23158 A:0.30105 G:0.20421 position 3: T:0.42105 C:0.15158 A:0.28632 G:0.14105 Average T:0.28842 C:0.19158 A:0.27579 G:0.24421 #4: Phet26_DNA21 position 1: T:0.18105 C:0.19368 A:0.23368 G:0.39158 position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 position 3: T:0.41895 C:0.15789 A:0.28632 G:0.13684 Average T:0.28842 C:0.19368 A:0.27368 G:0.24421 #5: Pmex37_DNA21 position 1: T:0.18105 C:0.19158 A:0.23789 G:0.38947 position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 position 3: T:0.41895 C:0.15789 A:0.28211 G:0.14105 Average T:0.28842 C:0.19298 A:0.27368 G:0.24491 #6: Ptre197_DNA2 position 1: T:0.18105 C:0.19158 A:0.24000 G:0.38737 position 2: T:0.26316 C:0.23158 A:0.30105 G:0.20421 position 3: T:0.42316 C:0.15158 A:0.28421 G:0.14105 Average T:0.28912 C:0.19158 A:0.27509 G:0.24421 #7: WHR1_DNA225 position 1: T:0.18105 C:0.19158 A:0.23579 G:0.39158 position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 position 3: T:0.41684 C:0.15579 A:0.28211 G:0.14526 Average T:0.28772 C:0.19228 A:0.27298 G:0.24702 #8: YALD273_DNA5 position 1: T:0.18105 C:0.19368 A:0.23368 G:0.39158 position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 position 3: T:0.41895 C:0.15789 A:0.28632 G:0.13684 Average T:0.28842 C:0.19368 A:0.27368 G:0.24421 #9: Pop_trich_ch position 1: T:0.18105 C:0.19368 A:0.23368 G:0.39158 position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 position 3: T:0.41895 C:0.15789 A:0.28632 G:0.13684 Average T:0.28842 C:0.19368 A:0.27368 G:0.24421 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 126 | Ser S TCT 53 | Tyr Y TAT 117 | Cys C TGT 45 TTC 72 | TCC 37 | TAC 36 | TGC 27 Leu L TTA 81 | TCA 9 | *** * TAA 0 | *** * TGA 0 TTG 90 | TCG 9 | TAG 0 | Trp W TGG 72 ------------------------------------------------------------------------------ Leu L CTT 81 | Pro P CCT 99 | His H CAT 81 | Arg R CGT 99 CTC 0 | CCC 52 | CAC 45 | CGC 45 CTA 84 | CCA 27 | Gln Q CAA 88 | CGA 54 CTG 33 | CCG 18 | CAG 18 | CGG 0 ------------------------------------------------------------------------------ Ile I ATT 92 | Thr T ACT 152 | Asn N AAT 81 | Ser S AGT 16 ATC 77 | ACC 72 | AAC 54 | AGC 27 ATA 18 | ACA 47 | Lys K AAA 162 | Arg R AGA 54 Met M ATG 87 | ACG 9 | AAG 54 | AGG 9 ------------------------------------------------------------------------------ Val V GTT 131 | Ala A GCT 215 | Asp D GAT 198 | Gly G GGT 207 GTC 9 | GCC 44 | GAC 51 | GGC 18 GTA 115 | GCA 141 | Glu E GAA 218 | GGA 117 GTG 36 | GCG 1 | GAG 84 | GGG 81 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.18105 C:0.19275 A:0.23649 G:0.38971 position 2: T:0.26480 C:0.23041 A:0.30105 G:0.20374 position 3: T:0.41942 C:0.15579 A:0.28421 G:0.14058 Average T:0.28842 C:0.19298 A:0.27392 G:0.24468 Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): 0.02080748 0.00772882 0.01409988 0.00697451 0.01810545 0.00672517 0.01226889 0.00606881 0.02365656 0.00878710 0.00000000 0.00000000 0.01601000 0.00594683 0.00000000 0.00536643 0.02215163 0.00822810 0.01501073 0.00742506 0.01927505 0.00715961 0.01306145 0.00646085 0.02518476 0.00935474 0.01706608 0.00844174 0.01704423 0.00633099 0.01154977 0.00571310 0.02717876 0.01009540 0.01841729 0.00911012 0.02364937 0.00878443 0.01602564 0.00792709 0.03090024 0.01147772 0.02093909 0.01035753 0.02091228 0.00776775 0.01417090 0.00700964 0.04478716 0.01663594 0.03034936 0.01501232 0.03897116 0.01447562 0.02640823 0.01306284 0.05091968 0.01891383 0.03450497 0.01706789 0.03446079 0.01280027 0.02335185 0.01155100 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later ML. analysis. Use runmode = -2 for ML pairwise comparison.) Pdel181_DNA2 Pfre186_DNA2aaaaaaaa-1.0300 (0.0009 0.0000) Pgra187_DNA2 1.0623 (0.0093 0.0088) 1.1684 (0.0102 0.0088) Phet26_DNA21 1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117) Pmex37_DNA21 -1.0000 (0.0046 0.0000)-1.0000 (0.0037 0.0000) 0.9534 (0.0084 0.0088) 0.9555 (0.0028 0.0029) Ptre197_DNA2 1.5965 (0.0093 0.0058) 1.7561 (0.0102 0.0058) 0.0000 (0.0000 0.0088) 0.6357 (0.0056 0.0088) 1.4328 (0.0084 0.0058) WHR1_DNA225 0.7964 (0.0046 0.0058) 0.9557 (0.0056 0.0058) 0.4430 (0.0065 0.0147) 0.3175 (0.0028 0.0088) 0.6354 (0.0037 0.0058) 0.5548 (0.0065 0.0117) YALD273_DNA5 1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117)-1.0000 (0.0000 0.0000) 0.9555 (0.0028 0.0029) 0.6357 (0.0056 0.0088) 0.3175 (0.0028 0.0088) Pop_trich_ch 1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117)-1.0000 (0.0000 0.0000) 0.9555 (0.0028 0.0029) 0.6357 (0.0056 0.0088) 0.3175 (0.0028 0.0088)-1.0000 (0.0000 0.0000) pairwise comparison, codon frequencies: F3x4. 2 (Pfre186_DNA2) ... 1 (Pdel181_DNA2) lnL =-1891.391969 0.00214 999.00000 99.00000 t= 0.0021 S= 396.3 N= 1028.7 dN/dS= 99.0000 dN = 0.0010 dS = 0.0000 3 (Pgra187_DNA2) ... 1 (Pdel181_DNA2) lnL =-1968.029688 0.02808 3.26389 0.98370 t= 0.0281 S= 341.7 N= 1083.3 dN/dS= 0.9837 dN = 0.0093 dS = 0.0095 3 (Pgra187_DNA2) ... 2 (Pfre186_DNA2) lnL =-1972.711786 0.03025 3.71696 1.10191 t= 0.0302 S= 345.4 N= 1079.6 dN/dS= 1.1019 dN = 0.0103 dS = 0.0094 4 (Phet26_DNA21) ... 1 (Pdel181_DNA2) lnL =-1921.561815 0.01073 3.11375 1.18654 t= 0.0107 S= 342.5 N= 1082.5 dN/dS= 1.1865 dN = 0.0037 dS = 0.0031 4 (Phet26_DNA21) ... 2 (Pfre186_DNA2) lnL =-1927.106138 0.01287 4.25522 1.54964 t= 0.0129 S= 352.0 N= 1073.0 dN/dS= 1.5496 dN = 0.0047 dS = 0.0030 4 (Phet26_DNA21) ... 3 (Pgra187_DNA2) lnL =-1948.501568 0.02179 4.30601 0.45869 t= 0.0218 S= 349.8 N= 1075.2 dN/dS= 0.4587 dN = 0.0056 dS = 0.0123 5 (Pmex37_DNA21) ... 1 (Pdel181_DNA2) lnL =-1920.298777 0.01053 1.55733 99.00000 t= 0.0105 S= 318.9 N= 1106.1 dN/dS= 99.0000 dN = 0.0045 dS = 0.0000 5 (Pmex37_DNA21) ... 2 (Pfre186_DNA2) lnL =-1914.616800 0.00838 0.77696 99.00000 t= 0.0084 S= 296.5 N= 1128.5 dN/dS= 99.0000 dN = 0.0035 dS = 0.0000 5 (Pmex37_DNA21) ... 3 (Pgra187_DNA2) lnL =-1960.971487 0.02594 4.03558 0.91514 t= 0.0259 S= 348.1 N= 1076.9 dN/dS= 0.9151 dN = 0.0085 dS = 0.0092 5 (Pmex37_DNA21) ... 4 (Phet26_DNA21) lnL =-1913.389962 0.00862 6.08298 0.97563 t= 0.0086 S= 362.3 N= 1062.7 dN/dS= 0.9756 dN = 0.0029 dS = 0.0029 6 (Ptre197_DNA2) ... 1 (Pdel181_DNA2) lnL =-1961.098136 0.02585 4.25957 1.53161 t= 0.0258 S= 349.5 N= 1075.5 dN/dS= 1.5316 dN = 0.0094 dS = 0.0061 6 (Ptre197_DNA2) ... 2 (Pfre186_DNA2) lnL =-1965.694050 0.02802 4.83643 1.71212 t= 0.0280 S= 352.8 N= 1072.2 dN/dS= 1.7121 dN = 0.0104 dS = 0.0061 6 (Ptre197_DNA2) ... 3 (Pgra187_DNA2) lnL =-1901.130192 0.00676 4.05781 0.00100 t= 0.0068 S= 345.2 N= 1079.8 dN/dS= 0.0010 dN = 0.0000 dS = 0.0093 6 (Ptre197_DNA2) ... 4 (Phet26_DNA21) lnL =-1941.618065 0.01954 6.78012 0.64571 t= 0.0195 S= 361.6 N= 1063.4 dN/dS= 0.6457 dN = 0.0057 dS = 0.0089 6 (Ptre197_DNA2) ... 5 (Pmex37_DNA21) lnL =-1953.852896 0.02372 5.63419 1.43296 t= 0.0237 S= 357.2 N= 1067.8 dN/dS= 1.4330 dN = 0.0086 dS = 0.0060 7 (WHR1_DNA225) ... 1 (Pdel181_DNA2) lnL =-1936.561781 0.01511 2.61161 0.72506 t= 0.0151 S= 337.6 N= 1087.4 dN/dS= 0.7251 dN = 0.0046 dS = 0.0064 7 (WHR1_DNA225) ... 2 (Pfre186_DNA2) lnL =-1941.975543 0.01725 3.35589 0.90347 t= 0.0172 S= 345.7 N= 1079.3 dN/dS= 0.9035 dN = 0.0056 dS = 0.0062 7 (WHR1_DNA225) ... 3 (Pgra187_DNA2) lnL =-1960.455637 0.02624 3.64066 0.41889 t= 0.0262 S= 345.9 N= 1079.1 dN/dS= 0.4189 dN = 0.0065 dS = 0.0156 7 (WHR1_DNA225) ... 4 (Phet26_DNA21) lnL =-1928.593448 0.01318 1.68562 0.26826 t= 0.0132 S= 322.2 N= 1102.8 dN/dS= 0.2683 dN = 0.0027 dS = 0.0101 7 (WHR1_DNA225) ... 5 (Pmex37_DNA21) lnL =-1928.718524 0.01300 3.82266 0.60956 t= 0.0130 S= 350.1 N= 1074.9 dN/dS= 0.6096 dN = 0.0037 dS = 0.0061 7 (WHR1_DNA225) ... 6 (Ptre197_DNA2) lnL =-1954.005346 0.02397 5.04975 0.54692 t= 0.0240 S= 355.1 N= 1069.9 dN/dS= 0.5469 dN = 0.0066 dS = 0.0121 8 (YALD273_DNA5) ... 1 (Pdel181_DNA2) lnL =-1921.561815 0.01073 3.11377 1.18654 t= 0.0107 S= 342.5 N= 1082.5 dN/dS= 1.1865 dN = 0.0037 dS = 0.0031 8 (YALD273_DNA5) ... 2 (Pfre186_DNA2) lnL =-1927.106138 0.01287 4.25516 1.54964 t= 0.0129 S= 352.0 N= 1073.0 dN/dS= 1.5496 dN = 0.0047 dS = 0.0030 8 (YALD273_DNA5) ... 3 (Pgra187_DNA2) lnL =-1948.501568 0.02179 4.30601 0.45869 t= 0.0218 S= 349.8 N= 1075.2 dN/dS= 0.4587 dN = 0.0056 dS = 0.0123 8 (YALD273_DNA5) ... 4 (Phet26_DNA21) lnL =-1881.846112 0.00001 8.33165 0.18598 t= 0.0000 S= 369.5 N= 1055.5 dN/dS= 0.1860 dN = 0.0000 dS = 0.0000 8 (YALD273_DNA5) ... 5 (Pmex37_DNA21) lnL =-1913.389962 0.00862 6.08296 0.97563 t= 0.0086 S= 362.3 N= 1062.7 dN/dS= 0.9756 dN = 0.0029 dS = 0.0029 8 (YALD273_DNA5) ... 6 (Ptre197_DNA2) lnL =-1941.618065 0.01954 6.78014 0.64571 t= 0.0195 S= 361.6 N= 1063.4 dN/dS= 0.6457 dN = 0.0057 dS = 0.0089 8 (YALD273_DNA5) ... 7 (WHR1_DNA225) lnL =-1928.593448 0.01318 1.68561 0.26826 t= 0.0132 S= 322.2 N= 1102.8 dN/dS= 0.2683 dN = 0.0027 dS = 0.0101 9 (Pop_trich_ch) ... 1 (Pdel181_DNA2) lnL =-1921.561815 0.01073 3.11378 1.18654 t= 0.0107 S= 342.5 N= 1082.5 dN/dS= 1.1865 dN = 0.0037 dS = 0.0031 9 (Pop_trich_ch) ... 2 (Pfre186_DNA2) lnL =-1927.106138 0.01287 4.25517 1.54964 t= 0.0129 S= 352.0 N= 1073.0 dN/dS= 1.5496 dN = 0.0047 dS = 0.0030 9 (Pop_trich_ch) ... 3 (Pgra187_DNA2) lnL =-1948.501568 0.02179 4.30599 0.45869 t= 0.0218 S= 349.8 N= 1075.2 dN/dS= 0.4587 dN = 0.0056 dS = 0.0123 9 (Pop_trich_ch) ... 4 (Phet26_DNA21) lnL =-1881.845859 0.00001 0.40000 0.00100 t= 0.0000 S= 281.0 N= 1144.0 dN/dS= 0.0010 dN = 0.0000 dS = 0.0000 9 (Pop_trich_ch) ... 5 (Pmex37_DNA21) lnL =-1913.389962 0.00862 6.08299 0.97562 t= 0.0086 S= 362.3 N= 1062.7 dN/dS= 0.9756 dN = 0.0029 dS = 0.0029 9 (Pop_trich_ch) ... 6 (Ptre197_DNA2) lnL =-1941.618065 0.01954 6.78013 0.64571 t= 0.0195 S= 361.6 N= 1063.4 dN/dS= 0.6457 dN = 0.0057 dS = 0.0089 9 (Pop_trich_ch) ... 7 (WHR1_DNA225) lnL =-1928.593448 0.01318 1.68561 0.26826 t= 0.0132 S= 322.2 N= 1102.8 dN/dS= 0.2683 dN = 0.0027 dS = 0.0101 9 (Pop_trich_ch) ... 8 (YALD273_DNA5) lnL =-1881.846052 0.00001 0.40000 0.16519 t= 0.0000 S= 281.0 N= 1144.0 dN/dS= 0.1652 dN = 0.0000 dS = 0.0000 Bio-Tools-Phylo-PAML-1.7.3/t/data/bug3331.mlc0000644000175000017500000001463713316145226021127 0ustar carandraugcarandraug 2 195 seq1 GTT ACC GGT CTT GAC ATG AAC ATC AGC CAA TTT CTA AAA AGC CTT GGC CTT GAA CAC CTT CGG GAT ATC TTT GAA ACA GAA CAG ATT ACA CTA GAT GTG TTG GCT GAT ATG GGT CAT GAA GAG TTG AAA GAA ATA GGC ATC AAT GCA TAT GGG CAC CGC CAC AAA TTA ATC AAA GGA GTA GAA AGA CTT TTA GGT seq2 GTT GCT GGT CTT GAC ATG AAT ATC AGC CAA TTT CTA AAA AGC CTT GGC CTT GAA CAC CTT CGG GAT ATC TTT GAA ACA GAA CAG ATT ACA CTA GAT GTG TTG GCT GAT ATG GGT CAT GAA GAG TTG AAA GAA ATA GGC ATC AAT GCA TAT GGG CAC CGC CAC AAA TTA ATC AAA GGA GTA GAA AGA CTC TTA GGT Printing out site pattern counts 2 111 P seq1 AAA AAC AAT ACA ACC AGA AGC ATA ATC ATG ATT CAA CAC CAG CAT CGC CGG CTA CTT CTT GAA GAC GAG GAT GCA GCT GGA GGC GGG GGT GTA GTG GTT TAT TTA TTG TTT seq2 ... ..T ... ... G.T ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 4 1 1 2 1 1 2 1 4 2 1 1 3 1 1 1 1 2 1 4 6 1 1 3 1 1 1 2 1 3 1 1 1 1 2 2 2 CODONML (in paml version 4.5, December 2011) /var/folders/pr/wb88nxq93xn7hdhgr2_bjd5w0000gn/T/UIa4SSyGGv/Bw_1hNQpYZ Model: One dN/dS ratio for branches kappa = 2.000 fixed Codon frequency model: F3x4 ns = 2 ls = 65 Codon usage in sequences -------------------------------------------------------------- Phe TTT 2 2 | Ser TCT 0 0 | Tyr TAT 1 1 | Cys TGT 0 0 TTC 0 0 | TCC 0 0 | TAC 0 0 | TGC 0 0 Leu TTA 2 2 | TCA 0 0 | *** TAA 0 0 | *** TGA 0 0 TTG 2 2 | TCG 0 0 | TAG 0 0 | Trp TGG 0 0 -------------------------------------------------------------- Leu CTT 5 4 | Pro CCT 0 0 | His CAT 1 1 | Arg CGT 0 0 CTC 0 1 | CCC 0 0 | CAC 3 3 | CGC 1 1 CTA 2 2 | CCA 0 0 | Gln CAA 1 1 | CGA 0 0 CTG 0 0 | CCG 0 0 | CAG 1 1 | CGG 1 1 -------------------------------------------------------------- Ile ATT 1 1 | Thr ACT 0 0 | Asn AAT 1 2 | Ser AGT 0 0 ATC 4 4 | ACC 1 0 | AAC 1 0 | AGC 2 2 ATA 1 1 | ACA 2 2 | Lys AAA 4 4 | Arg AGA 1 1 Met ATG 2 2 | ACG 0 0 | AAG 0 0 | AGG 0 0 -------------------------------------------------------------- Val GTT 1 1 | Ala GCT 1 2 | Asp GAT 3 3 | Gly GGT 3 3 GTC 0 0 | GCC 0 0 | GAC 1 1 | GGC 2 2 GTA 1 1 | GCA 1 1 | Glu GAA 6 6 | GGA 1 1 GTG 1 1 | GCG 0 0 | GAG 1 1 | GGG 1 1 -------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: seq1 position 1: T:0.10769 C:0.23077 A:0.30769 G:0.35385 position 2: T:0.36923 C:0.07692 A:0.36923 G:0.18462 position 3: T:0.29231 C:0.23077 A:0.33846 G:0.13846 Average T:0.25641 C:0.17949 A:0.33846 G:0.22564 #2: seq2 position 1: T:0.10769 C:0.23077 A:0.29231 G:0.36923 position 2: T:0.36923 C:0.07692 A:0.36923 G:0.18462 position 3: T:0.30769 C:0.21538 A:0.33846 G:0.13846 Average T:0.26154 C:0.17436 A:0.33333 G:0.23077 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 4 | Ser S TCT 0 | Tyr Y TAT 2 | Cys C TGT 0 TTC 0 | TCC 0 | TAC 0 | TGC 0 Leu L TTA 4 | TCA 0 | *** * TAA 0 | *** * TGA 0 TTG 4 | TCG 0 | TAG 0 | Trp W TGG 0 ------------------------------------------------------------------------------ Leu L CTT 9 | Pro P CCT 0 | His H CAT 2 | Arg R CGT 0 CTC 1 | CCC 0 | CAC 6 | CGC 2 CTA 4 | CCA 0 | Gln Q CAA 2 | CGA 0 CTG 0 | CCG 0 | CAG 2 | CGG 2 ------------------------------------------------------------------------------ Ile I ATT 2 | Thr T ACT 0 | Asn N AAT 3 | Ser S AGT 0 ATC 8 | ACC 1 | AAC 1 | AGC 4 ATA 2 | ACA 4 | Lys K AAA 8 | Arg R AGA 2 Met M ATG 4 | ACG 0 | AAG 0 | AGG 0 ------------------------------------------------------------------------------ Val V GTT 2 | Ala A GCT 3 | Asp D GAT 6 | Gly G GGT 6 GTC 0 | GCC 0 | GAC 2 | GGC 4 GTA 2 | GCA 2 | Glu E GAA 12 | GGA 2 GTG 2 | GCG 0 | GAG 2 | GGG 2 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.10769 C:0.23077 A:0.30000 G:0.36154 position 2: T:0.36923 C:0.07692 A:0.36923 G:0.18462 position 3: T:0.30000 C:0.22308 A:0.33846 G:0.13846 Average T:0.25897 C:0.17692 A:0.33590 G:0.22821 Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): 0.01224357 0.00910419 0.01381326 0.00565088 0.00255074 0.00189671 0.00287776 0.00117727 0.01224357 0.00910419 0.00000000 0.00000000 0.00612179 0.00455210 0.00000000 0.00282544 0.02623622 0.01950899 0.02959984 0.01210903 0.00546588 0.00406437 0.00616663 0.00252271 0.02623622 0.01950899 0.02959984 0.01210903 0.01311811 0.00975449 0.01479992 0.00605451 0.03410709 0.02536168 0.03847979 0.01574173 0.00710564 0.00528368 0.00801662 0.00327953 0.03410709 0.02536168 0.03847979 0.01574173 0.01705355 0.01268084 0.01923990 0.00787087 0.04110342 0.03056408 0.04637309 0.01897081 0.00856321 0.00636752 0.00966106 0.00395225 0.04110342 0.03056408 0.04637309 0.01897081 0.02055171 0.01528204 0.02318654 0.00948540 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later ML. analysis. Use runmode = -2 for ML pairwise comparison.) seq1 seq2 0.0913 (0.0066 0.0726) pairwise comparison, codon frequencies: F3x4. 2 (seq2) ... 1 (seq1) lnL = -272.706911 0.06846 0.10294 t= 0.0685 S= 51.9 N= 143.1 dN/dS= 0.1029 dN = 0.0069 dS = 0.0668 Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml_nssites.mlc0000644000175000017500000005320413316145226023044 0ustar carandraugcarandraug Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAC AAC ACA CGA GCT ACA AAC TAC AAT GCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AGT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG Hla_gibbon AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCC GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT CTC CGT CAG TAT ATT CAA GGT TGT GGA GTA Cgu/Can_colobus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAC GCT ACA AAC TAC AAT CCT GGA GAT GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AAA AAG CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTA Pne_langur AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT GAT GCC TGT CAT ATA TCC TGC AGT GCT TTG CTG CAA AAC AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC GTT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AAA GAT GTC AGT CAG TAC GTT AAA GGT TGT GGA GTG Mmu_rhesus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT AAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA ACT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG Ssc_squirrelM AAG GTC TTC GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG CTT GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAC TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT CAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA Cja_marmoset AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAC AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGG GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA CODONML (in paml 3.13, August 2002) lysozymeSmall.txt Model: One dN/dS ratio dGamma (ncatG=11) Codon frequencies: F3x4 Warning: Gamma model for codons. See documentation.Site-class models ns = 7 ls = 130 # site patterns = 81 2 1 1 1 2 7 2 3 3 1 2 2 2 1 1 5 1 4 3 2 1 1 3 1 5 4 5 1 1 1 1 2 1 3 2 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 2 2 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG ATC AGC CTA GCA AAC TGG ATG AGT GGT TAC ACA CGA GCT AAT GCT GAC AGA TAT GGG ATA TTT CAG ATC CGC TAC AAT GAT AAA ACC CCA GTT AAT CAT TTA TCC TGC AGT CAA GAT AAC GCT GAT GTA GCT GTC CGT ATT AGA GTG AGA AAT CGT AGA GTC CGT TAT GTT CAA GGT GTG Hla_gibbon ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ..C ... ... ... ... ..C ... ... ... ... ... ... ... C.. ... ... A.. ... ... ..A Cgu/Can_colobus ... A.. ... ... ... ... ... ... ... ... ... ... ... .A. ... ... C.. ... ... ... .A. G.. ... ... ... ... ... G.. ... ... ..T ... GAC ... ... C.. ..T GA. ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... A.. ... ... .A. ... A.. ... ... ... ... ... ... A.. ... C.. ... .A. ..G .AC ... ... A.. ... ... G.. ... ..A Pne_langur ... A.. ... ... ... ... ... ... ... ... ... ... ... .A. ... ... C.. ... ... ... .A. G.. ... ... ... ... ... G.. ... ... ..T ... GA. ... ... C.. ... GA. ... ... ... ... ... ... ... ... ... A.. ... ... ... ... G.. ... A.. ... ... ... ... A.C ... ... ... ... ... ... A.. G.. C.. ... ... ... .AC .A. ... A.. ..C ... A.. ... ... Mmu_rhesus ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... G.. ... AA. ..T ... .A. ... ... C.. ... CA. ... ... ... ... ... ... .A. ... ... A.. ... ... ... ... ... ... A.. ... ... .A. ... ... ... ... ... ... A.. ... A.. ... ... ... ... ... .AC ... ... A.. ... ... ... ... ... Ssc_squirrelM ... ... ..C ... ... ... ... ... ... ... ... ... ... ..G C.T ... ... ... ... ... ... ... ... ... ... ... ... ... ... .AC ..T ... ..T ... ... C.. ... CA. ... ... ... ... ... ... .A. ..T ... A.. .G. ... ... ... ... ... A.. ... ... .A. ... ... G.. A.. C.A ..G ..C ... ... ... ... ... .A. GC. .A. ... ... A.. ... ... ... ... ..A Cja_marmoset ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ..T ... C.. ... ... ... ... ... ... ... ... ... ... ... ... .A. ..T ... ..T ... ... C.. ... CA. ... ... ... ... ... ... .A. ..T ..C A.. .G. ... ... ... ... ... A.. ... ... .A. ... ... G.. A.. ..A ..G ..C ... ..C ... ..G ... .A. GC. .A. ... ... A.. ... ... ... ... ..A Codon usage in sequences -------------------------------------------------------------------------------------------------------------- Phe TTT 2 2 2 2 2 1 | Ser TCT 0 0 0 0 0 0 | Tyr TAT 2 3 3 2 3 4 | Cys TGT 7 7 7 7 7 7 TTC 0 0 0 0 0 1 | TCC 1 1 1 1 1 1 | TAC 4 3 3 4 3 2 | TGC 1 1 1 1 1 1 Leu TTA 1 1 0 0 0 0 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 TTG 4 4 4 4 4 3 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 5 5 5 5 5 5 -------------------------------------------------------------------------------------------------------------- Leu CTT 0 0 0 0 0 1 | Pro CCT 0 1 1 1 1 1 | His CAT 1 1 1 1 1 2 | Arg CGT 3 2 0 0 0 2 CTC 0 1 0 0 0 0 | CCC 0 0 0 0 0 0 | CAC 0 0 1 1 2 1 | CGC 1 2 1 1 0 0 CTA 1 1 1 1 1 1 | CCA 2 2 2 2 2 2 | Gln CAA 4 4 3 3 6 6 | CGA 1 1 1 1 0 0 CTG 2 2 3 3 3 2 | CCG 0 0 0 0 0 0 | CAG 2 2 2 2 2 2 | CGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------- Ile ATT 1 2 1 0 1 1 | Thr ACT 2 2 2 2 3 3 | Asn AAT 5 6 7 5 8 6 | Ser AGT 2 1 3 4 3 2 ATC 3 3 3 3 4 3 | ACC 1 1 1 1 1 1 | AAC 5 5 5 6 5 4 | AGC 3 3 3 3 3 3 ATA 1 1 2 2 2 2 | ACA 2 2 2 2 2 2 | Lys AAA 3 3 5 6 3 3 | Arg AGA 6 6 2 2 5 4 Met ATG 2 2 0 0 0 2 | ACG 0 0 0 0 0 0 | AAG 2 2 4 3 2 2 | AGG 3 3 2 2 3 4 -------------------------------------------------------------------------------------------------------------- Val GTT 3 2 3 4 3 3 | Ala GCT 6 4 5 5 4 4 | Asp GAT 7 7 6 6 6 5 | Gly GGT 2 2 2 2 1 1 GTC 3 2 3 3 2 3 | GCC 3 4 3 3 3 4 | GAC 1 1 1 1 1 3 | GGC 3 3 3 3 3 3 GTA 1 2 2 1 1 1 | GCA 5 5 5 5 5 5 | Glu GAA 1 1 3 3 1 1 | GGA 5 5 5 5 5 5 GTG 2 1 2 3 3 2 | GCG 0 0 0 0 0 0 | GAG 2 2 2 2 2 2 | GGG 1 1 1 1 1 1 -------------------------------------------------------------------------------------------------------------- -------------------------------------------------- Phe TTT 3 | Ser TCT 0 | Tyr TAT 4 | Cys TGT 7 TTC 0 | TCC 1 | TAC 2 | TGC 1 Leu TTA 0 | TCA 0 | *** TAA 0 | *** TGA 0 TTG 3 | TCG 0 | TAG 0 | Trp TGG 5 -------------------------------------------------- Leu CTT 0 | Pro CCT 1 | His CAT 2 | Arg CGT 1 CTC 0 | CCC 0 | CAC 1 | CGC 1 CTA 1 | CCA 2 | Gln CAA 5 | CGA 0 CTG 3 | CCG 0 | CAG 2 | CGG 0 -------------------------------------------------- Ile ATT 1 | Thr ACT 3 | Asn AAT 5 | Ser AGT 2 ATC 3 | ACC 1 | AAC 5 | AGC 3 ATA 2 | ACA 2 | Lys AAA 3 | Arg AGA 3 Met ATG 1 | ACG 0 | AAG 2 | AGG 5 -------------------------------------------------- Val GTT 3 | Ala GCT 4 | Asp GAT 6 | Gly GGT 1 GTC 3 | GCC 4 | GAC 2 | GGC 3 GTA 1 | GCA 5 | Glu GAA 2 | GGA 5 GTG 2 | GCG 0 | GAG 2 | GGG 1 -------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: Hsa_Human position 1: T:0.20769 C:0.13077 A:0.31538 G:0.34615 position 2: T:0.20000 C:0.16923 A:0.30000 G:0.33077 position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231 #2: Hla_gibbon position 1: T:0.20769 C:0.14615 A:0.32308 G:0.32308 position 2: T:0.20000 C:0.16923 A:0.30769 G:0.32308 position 3: T:0.32308 C:0.23077 A:0.26154 G:0.18462 #3: Cgu/Can_colobus position 1: T:0.20000 C:0.12308 A:0.32308 G:0.35385 position 2: T:0.20000 C:0.16923 A:0.35385 G:0.27692 position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231 #4: Pne_langur position 1: T:0.20000 C:0.12308 A:0.31538 G:0.36154 position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462 position 3: T:0.31538 C:0.23846 A:0.25385 G:0.19231 #5: Mmu_rhesus position 1: T:0.20000 C:0.13846 A:0.34615 G:0.31538 position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462 position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231 #6: Ssc_squirrelM position 1: T:0.19231 C:0.15385 A:0.32308 G:0.33077 position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231 position 3: T:0.33077 C:0.23077 A:0.24615 G:0.19231 #7: Cja_marmoset position 1: T:0.20000 C:0.14615 A:0.31538 G:0.33846 position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231 position 3: T:0.33077 C:0.23077 A:0.23846 G:0.20000 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 14 | Ser S TCT 0 | Tyr Y TAT 21 | Cys C TGT 49 TTC 1 | TCC 7 | TAC 21 | TGC 7 Leu L TTA 2 | TCA 0 | *** * TAA 0 | *** * TGA 0 TTG 26 | TCG 0 | TAG 0 | Trp W TGG 35 ------------------------------------------------------------------------------ Leu L CTT 1 | Pro P CCT 6 | His H CAT 9 | Arg R CGT 8 CTC 1 | CCC 0 | CAC 6 | CGC 6 CTA 7 | CCA 14 | Gln Q CAA 31 | CGA 4 CTG 18 | CCG 0 | CAG 14 | CGG 0 ------------------------------------------------------------------------------ Ile I ATT 7 | Thr T ACT 17 | Asn N AAT 42 | Ser S AGT 17 ATC 22 | ACC 7 | AAC 35 | AGC 21 ATA 12 | ACA 14 | Lys K AAA 26 | Arg R AGA 28 Met M ATG 7 | ACG 0 | AAG 17 | AGG 22 ------------------------------------------------------------------------------ Val V GTT 21 | Ala A GCT 32 | Asp D GAT 43 | Gly G GGT 11 GTC 19 | GCC 24 | GAC 10 | GGC 21 GTA 9 | GCA 35 | Glu E GAA 12 | GGA 35 GTG 15 | GCG 0 | GAG 14 | GGG 7 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.20110 C:0.13736 A:0.32308 G:0.33846 position 2: T:0.20000 C:0.17143 A:0.33077 G:0.29780 position 3: T:0.32747 C:0.22857 A:0.25165 G:0.19231 Codon frequencies under model, for use in evolver: 0.01378574 0.00962226 0.01059374 0.00809565 0.01181635 0.00824765 0.00908035 0.00693913 0.02279949 0.01591374 0.00000000 0.00000000 0.02052711 0.01432765 0.00000000 0.01205451 0.00941649 0.00657258 0.00723616 0.00552982 0.00807127 0.00563364 0.00620242 0.00473984 0.01557342 0.01087004 0.01196749 0.00914546 0.01402125 0.00978665 0.01077472 0.00823396 0.02214758 0.01545871 0.01701945 0.01300613 0.01898364 0.01325032 0.01458810 0.01114811 0.03662868 0.02556633 0.02814755 0.02151013 0.03297798 0.02301819 0.02534214 0.01936627 0.02320222 0.01619484 0.01782990 0.01362547 0.01988762 0.01388129 0.01528277 0.01167897 0.03837291 0.02678377 0.02948791 0.02253443 0.03454836 0.02411429 0.02654891 0.02028847 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) Hsa_Human Hla_gibbon 0.2782 (0.0133 0.0478) Cgu/Can_colobus 1.1086 (0.0742 0.0670) 1.1055 (0.0742 0.0671) Pne_langur 1.1979 (0.0725 0.0605) 0.9234 (0.0797 0.0863) 0.5517 (0.0267 0.0484) Mmu_rhesus 1.8744 (0.0562 0.0300) 1.0215 (0.0561 0.0550) 1.2973 (0.0473 0.0364) 1.3970 (0.0508 0.0364) Ssc_squirrelM 0.4701 (0.0633 0.1346) 0.4688 (0.0633 0.1349) 0.5159 (0.0775 0.1502) 0.5833 (0.0959 0.1645) 0.4544 (0.0559 0.1230) Cja_marmoset 0.4725 (0.0634 0.1341) 0.5925 (0.0633 0.1069) 0.4702 (0.0704 0.1496) 0.5411 (0.0886 0.1638) 0.3995 (0.0490 0.1225) 0.1595 (0.0099 0.0619) Model 0: one-ratio TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 check convergence.. lnL(ntime: 11 np: 14): -906.017440 +0.000000 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7 0.06798 0.02556 0.03889 0.04345 0.07637 0.04379 0.05254 0.02168 0.12266 0.04080 0.02392 4.54006 0.80663 0.50000 SEs for parameters: 0.02557 0.01516 0.01844 0.02016 0.02668 0.01990 0.02155 0.01551 0.03392 0.01916 0.01506 0.23600 0.23600 -1.00000 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 0.55765 ((1: 0.02556, 2: 0.03889): 0.06798, ((3: 0.04379, 4: 0.05254): 0.07637, 5: 0.02168): 0.04345, (6: 0.04080, 7: 0.02392): 0.12266); ((Hsa_Human: 0.02556, Hla_gibbon: 0.03889): 0.06798, ((Cgu/Can_colobus: 0.04379, Pne_langur: 0.05254): 0.07637, Mmu_rhesus: 0.02168): 0.04345, (Ssc_squirrelM: 0.04080, Cja_marmoset: 0.02392): 0.12266); Detailed output identifying parameters kappa (ts/tv) = 4.54006 alpha (gamma) = 0.50000 r ( 1): 1.00000 f: 1.00000 dN & dS for each branch branch t S N dN/dS dN dS S*dS N*dN 8..9 0.068 107.8 282.2 0.8066 0.0213 0.0263 2.8 6.0 9..1 0.026 107.8 282.2 0.8066 0.0080 0.0099 1.1 2.3 9..2 0.039 107.8 282.2 0.8066 0.0122 0.0151 1.6 3.4 8..10 0.043 107.8 282.2 0.8066 0.0136 0.0168 1.8 3.8 10..11 0.076 107.8 282.2 0.8066 0.0239 0.0296 3.2 6.7 11..3 0.044 107.8 282.2 0.8066 0.0137 0.0170 1.8 3.9 11..4 0.053 107.8 282.2 0.8066 0.0164 0.0204 2.2 4.6 10..5 0.022 107.8 282.2 0.8066 0.0068 0.0084 0.9 1.9 8..12 0.123 107.8 282.2 0.8066 0.0383 0.0475 5.1 10.8 12..6 0.041 107.8 282.2 0.8066 0.0128 0.0158 1.7 3.6 12..7 0.024 107.8 282.2 0.8066 0.0075 0.0093 1.0 2.1 Time used: 00:02:05 Model 1: neutral (2 categories) TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 lnL(ntime: 11 np: 14): -902.503869 +0.000000 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7 0.06961 0.02556 0.03938 0.04422 0.07778 0.04414 0.05228 0.02134 0.12574 0.04157 0.02367 4.29790 0.41271 0.50000 SEs for parameters: 0.02665 0.01541 0.01888 0.02101 0.02769 0.02034 0.02188 0.01585 0.03565 0.01971 0.01530 -1.00000 -1.00000 -1.00000 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 0.56528 ((1: 0.02556, 2: 0.03938): 0.06961, ((3: 0.04414, 4: 0.05228): 0.07778, 5: 0.02134): 0.04422, (6: 0.04157, 7: 0.02367): 0.12574); ((Hsa_Human: 0.02556, Hla_gibbon: 0.03938): 0.06961, ((Cgu/Can_colobus: 0.04414, Pne_langur: 0.05228): 0.07778, Mmu_rhesus: 0.02134): 0.04422, (Ssc_squirrelM: 0.04157, Cja_marmoset: 0.02367): 0.12574); Detailed output identifying parameters kappa (ts/tv) = 4.29790 dN/dS for site classes (K=2) p: 0.41271 0.58729 w: 0.00000 1.00000 alpha (gamma) = 0.41271 r ( 2): 0.00000 1.00000 f: 0.41271 0.58729 dN & dS for each branch branch t S N dN/dS dN dS S*dS N*dN 8..9 0.070 107.1 282.9 0.5873 0.0195 0.0331 3.5 5.5 9..1 0.026 107.1 282.9 0.5873 0.0071 0.0122 1.3 2.0 9..2 0.039 107.1 282.9 0.5873 0.0110 0.0187 2.0 3.1 8..10 0.044 107.1 282.9 0.5873 0.0124 0.0210 2.3 3.5 10..11 0.078 107.1 282.9 0.5873 0.0217 0.0370 4.0 6.1 11..3 0.044 107.1 282.9 0.5873 0.0123 0.0210 2.2 3.5 11..4 0.052 107.1 282.9 0.5873 0.0146 0.0249 2.7 4.1 10..5 0.021 107.1 282.9 0.5873 0.0060 0.0102 1.1 1.7 8..12 0.126 107.1 282.9 0.5873 0.0351 0.0598 6.4 9.9 12..6 0.042 107.1 282.9 0.5873 0.0116 0.0198 2.1 3.3 12..7 0.024 107.1 282.9 0.5873 0.0066 0.0113 1.2 1.9 Time used: 00:05:26 Model 2: selection (3 categories) TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 check convergence.. lnL(ntime: 11 np: 16): -900.076500 +0.000000 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7 0.07903 0.02598 0.04137 0.04535 0.08550 0.04486 0.05417 0.01935 0.13948 0.04319 0.02492 5.12250 0.38160 0.54916 6.17292 0.41271 SEs for parameters: 0.03226 0.01618 0.02021 0.02390 0.03229 0.02158 0.02363 0.01746 0.04358 0.02088 0.01602 1.50414 0.14016 0.16630 4.30113 -1.00000 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 0.60321 ((1: 0.02598, 2: 0.04137): 0.07903, ((3: 0.04486, 4: 0.05417): 0.08550, 5: 0.01935): 0.04535, (6: 0.04319, 7: 0.02492): 0.13948); ((Hsa_Human: 0.02598, Hla_gibbon: 0.04137): 0.07903, ((Cgu/Can_colobus: 0.04486, Pne_langur: 0.05417): 0.08550, Mmu_rhesus: 0.01935): 0.04535, (Ssc_squirrelM: 0.04319, Cja_marmoset: 0.02492): 0.13948); Detailed output identifying parameters kappa (ts/tv) = 5.12250 dN/dS for site classes (K=3) p: 0.38160 0.54916 0.06924 w: 0.00000 1.00000 6.17292 alpha (gamma) = 0.38160 r ( 3): 0.00000 1.00000 6.17292 f: 0.38160 0.54916 0.06924 dN & dS for each branch branch t S N dN/dS dN dS S*dS N*dN 8..9 0.079 109.3 280.7 0.9766 0.0262 0.0268 2.9 7.3 9..1 0.026 109.3 280.7 0.9766 0.0086 0.0088 1.0 2.4 9..2 0.041 109.3 280.7 0.9766 0.0137 0.0140 1.5 3.8 8..10 0.045 109.3 280.7 0.9766 0.0150 0.0154 1.7 4.2 10..11 0.086 109.3 280.7 0.9766 0.0283 0.0290 3.2 7.9 11..3 0.045 109.3 280.7 0.9766 0.0149 0.0152 1.7 4.2 11..4 0.054 109.3 280.7 0.9766 0.0179 0.0184 2.0 5.0 10..5 0.019 109.3 280.7 0.9766 0.0064 0.0066 0.7 1.8 8..12 0.139 109.3 280.7 0.9766 0.0462 0.0473 5.2 13.0 12..6 0.043 109.3 280.7 0.9766 0.0143 0.0146 1.6 4.0 12..7 0.025 109.3 280.7 0.9766 0.0083 0.0085 0.9 2.3 Positively selected sites Prob(w>1): 15 L 0.6588 17 M 0.6601 37 G 0.7155 41 R 0.9282 50 R 0.8292 62 R 0.5229 114 N 0.6491 126 Q 0.5226 Time used: 00:13:43 Bio-Tools-Phylo-PAML-1.7.3/t/data/cysprot.raxml.tre0000644000175000017500000000052513316145226022673 0ustar carandraugcarandraug(CATH_RAT:0.06724166276110664364,(ALEU_HORVU:0.56990248989280289926,(PAPA_CARPA:1.33742849612696801387,(CYS1_DICDI:1.03128829881092598519,(CATL_HUMAN:0.28192146236589338271,CATL_RAT:0.06484465365045161134):0.65573782483587061964):0.24929832020891837252):0.26104589965210051039):0.39109538627570700209,CATH_HUMAN:0.13768681658825404623):0.0; Bio-Tools-Phylo-PAML-1.7.3/t/data/aaml.mlc0000644000175000017500000000712613316145226020745 0ustar carandraugcarandraugAAML (in paml 3.12 February 2002) stewart.aa Model: Empirical (wag.dat) ns = 6 ls = 130 # site patterns = 98 4 1 1 1 1 8 2 1 6 1 1 3 1 1 1 1 1 4 2 1 1 3 1 4 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 1 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Langur KIFERCELAR TLKLGLDGYK VSNWVLAKWG NTETYNPGDE TDYIFQSRYN NGTPGAVDAH ISSALQNNIA DAVARVVSDP QIRVRNHQNK VSQVKGGV Baboon .......... ..R......R I........D ..Q......Q .......H.. D......N.. ..N...D..T .......... .........R ....Q... Human .V........ ..R..M...R I...M..... ..R...A..R .......... D......N.. L.....D... .......R.. ......R..R .R..Q... Rat .TY....F.. ..RN.MS..Y ..D....QHN ..QR.D...Q .......... D...R.KN.G .P....DD.T Q.IQ...R.. ....QR.K.R L.GIRN.. Cow .V........ .......... ....L.T..S ..K....SS. .......KW. D...N...G. V..EME.D.. K...KI..E- ..T.KS.RDH ..S.E.TL Horse .V.SK....H K.AQEM..FG Y....M.EYN ..RFGKNANG S..L..NKWK DN-RSSSN.N .M.K.DE..D .DIS...R.. KMSKVK.KD. L.ELASNL Frequencies.. A R N D C Q E G H I L K M F P S T W Y V Langur 0.1000 0.0462 0.0846 0.0538 0.0615 0.0385 0.0385 0.0846 0.0154 0.0462 0.0615 0.0692 0.0000 0.0154 0.0231 0.0615 0.0385 0.0385 0.0462 0.0769 Baboon 0.0923 0.0615 0.0846 0.0692 0.0615 0.0615 0.0231 0.0769 0.0231 0.0538 0.0615 0.0385 0.0000 0.0154 0.0231 0.0538 0.0462 0.0385 0.0462 0.0692 Human 0.1077 0.1077 0.0769 0.0615 0.0615 0.0462 0.0231 0.0846 0.0077 0.0385 0.0615 0.0385 0.0154 0.0154 0.0154 0.0462 0.0385 0.0385 0.0462 0.0692 Rat 0.0846 0.0923 0.0692 0.0692 0.0615 0.0692 0.0231 0.0769 0.0154 0.0538 0.0462 0.0462 0.0077 0.0154 0.0308 0.0538 0.0462 0.0308 0.0615 0.0462 Cow 0.0775 0.0233 0.0620 0.0543 0.0620 0.0155 0.0620 0.0620 0.0233 0.0388 0.0698 0.0930 0.0078 0.0155 0.0155 0.1008 0.0620 0.0465 0.0388 0.0698 Horse 0.0853 0.0310 0.1008 0.0775 0.0620 0.0155 0.0465 0.0543 0.0155 0.0233 0.0775 0.1163 0.0310 0.0388 0.0078 0.1008 0.0078 0.0388 0.0310 0.0388 Average 0.0913 0.0604 0.0797 0.0643 0.0617 0.0411 0.0360 0.0733 0.0167 0.0424 0.0630 0.0668 0.0103 0.0193 0.0193 0.0694 0.0398 0.0386 0.0450 0.0617 (Ambiguity characters are used to calculate freqs.) # constant sites: 46 (35.38%) AA distances (raw proportions of different sites) Langur Baboon 0.1077 Human 0.1385 0.1077 Rat 0.2923 0.2538 0.2846 Cow 0.2462 0.3000 0.3154 0.4231 Horse 0.5000 0.5000 0.4923 0.4923 0.5462 TREE # 1: (((1, 2), 3), 4, (5, 6)); MP score: -1 lnL(ntime: 9 np: 9): -1042.768973 +0.000000 7..8 8..9 9..1 9..2 8..3 7..4 7..10 10..5 10..6 0.00950 0.02220 0.08009 0.03337 0.06233 0.27133 0.09393 0.24105 0.58792 tree length = 1.40172 (((1:0.080088, 2:0.033370):0.022202, 3:0.062325):0.009497, 4:0.271333, (5:0.241055, 6:0.587920):0.093926); (((Langur:0.080088, Baboon:0.033370):0.022202, Human:0.062325):0.009497, Rat:0.271333, (Cow:0.241055, Horse:0.587920):0.093926); Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml_lysozyme/0000755000175000017500000000000013316145226022546 5ustar carandraugcarandraugBio-Tools-Phylo-PAML-1.7.3/t/data/codeml_lysozyme/2NG.dS0000644000175000017500000000051113316145226023421 0ustar carandraugcarandraug 7 Hsa_Human Hla_gibbon 0.0478 Cgu/Can_colobus 0.0670 0.0671 Pne_langur 0.0605 0.0863 0.0484 Mmu_rhesus 0.0300 0.0550 0.0364 0.0364 Ssc_squirrelM 0.1346 0.1349 0.1502 0.1645 0.1230 Cja_marmoset 0.1341 0.1069 0.1496 0.1638 0.1225 0.0619 Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml_lysozyme/2NG.tt0000644000175000017500000000051113316145226023502 0ustar carandraugcarandraug 7 Hsa_Human Hla_gibbon 0.0628 Cgu/Can_colobus 0.2179 0.2179 Pne_langur 0.2095 0.2435 0.0944 Mmu_rhesus 0.1514 0.1676 0.1348 0.1430 Ssc_squirrelM 0.2366 0.2366 0.2798 0.3324 0.2109 Cja_marmoset 0.2366 0.2186 0.2628 0.3150 0.1944 0.0633 Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml_lysozyme/lysozymeSmall.trees0000644000175000017500000000205613316145226026501 0ustar carandraugcarandraug2 ((Hsa_Human: 0.02556, Hla_gibbon: 0.03889): 0.06798, ((Cgu/Can_colobus: 0.04379, Pne_langur: 0.05254) #1 : 0.07637, Mmu_rhesus: 0.02168): 0.04345, (Ssc_squirrelM: 0.04080, Cja_marmoset: 0.02392): 0.12266); ((Hsa_Human: 0.02556, Hla_gibbon: 0.03889): 0.06798, ((Cgu/Can_colobus: 0.04379, Pne_langur: 0.05254) #1 : 0.07637, Mmu_rhesus: 0.02168): 0.04345, (Ssc_squirrelM: 0.04080, Cja_marmoset: 0.02392): 0.12266); ((Hsa_Human, Hla_gibbon),((Cgu/Can_colobus, Pne_langur) #1, Mmu_rhesus), (Ssc_squirrelM, Cja_marmoset)); / * table 1B&F */ ((1,2), ((3,4) #1, 5), (6,7) ); / * table 1B&F */ ((1,2) #1, ((3,4), 5), (6,7) ); / * table 1C&G */ ((1,2) #1, ((3,4) #1, 5), (6,7) ); / * table 1D&H */ ((1,2) #1, ((3,4) #2, 5), (6,7) ); / * table 1E&I */ ((1,2) #2, ((3,4) #1, 5), (6,7) ); / * table 1E&J */ ((1,2), ((3,4), 5), (6,7) ); For lysozymeSmall.nuc (Messier and Stewart 1997; Yang 1998) 1: Hsa_Human 2: Hla_gibbon 3: Cgu/Can_colobus 4: Pne_langur 5: Mmu_rhesus 6: Ssc_squirrelM 7: Cja_marmoset Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml_lysozyme/mlc0000644000175000017500000005040113316145226023244 0ustar carandraugcarandraug seed used = 162469585 Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAC AAC ACA CGA GCT ACA AAC TAC AAT GCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AGT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG Hla_gibbon AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCC GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT CTC CGT CAG TAT ATT CAA GGT TGT GGA GTA Cgu/Can_colobus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAC GCT ACA AAC TAC AAT CCT GGA GAT GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AAA AAG CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTA Pne_langur AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT GAT GCC TGT CAT ATA TCC TGC AGT GCT TTG CTG CAA AAC AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC GTT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AAA GAT GTC AGT CAG TAC GTT AAA GGT TGT GGA GTG Mmu_rhesus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT AAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA ACT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG Ssc_squirrelM AAG GTC TTC GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG CTT GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAC TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT CAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA Cja_marmoset AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAC AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGG GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA CODONML (in paml 3.14, January 2004) lysozymeSmall.txt Model: several dN/dS ratios for branches Codon frequencies: F3x4 ns = 7 ls = 130 # site patterns = 81 2 1 1 1 2 7 2 3 3 1 2 2 2 1 1 5 1 4 3 2 1 1 3 1 5 4 5 1 1 1 1 2 1 3 2 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 2 2 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG ATC AGC CTA GCA AAC TGG ATG AGT GGT TAC ACA CGA GCT AAT GCT GAC AGA TAT GGG ATA TTT CAG ATC CGC TAC AAT GAT AAA ACC CCA GTT AAT CAT TTA TCC TGC AGT CAA GAT AAC GCT GAT GTA GCT GTC CGT ATT AGA GTG AGA AAT CGT AGA GTC CGT TAT GTT CAA GGT GTG Hla_gibbon ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ..C ... ... ... ... ..C ... ... ... ... ... ... ... C.. ... ... A.. ... ... ..A Cgu/Can_colobus ... A.. ... ... ... ... ... ... ... ... ... ... ... .A. ... ... C.. ... ... ... .A. G.. ... ... ... ... ... G.. ... ... ..T ... GAC ... ... C.. ..T GA. ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... A.. ... ... .A. ... A.. ... ... ... ... ... ... A.. ... C.. ... .A. ..G .AC ... ... A.. ... ... G.. ... ..A Pne_langur ... A.. ... ... ... ... ... ... ... ... ... ... ... .A. ... ... C.. ... ... ... .A. G.. ... ... ... ... ... G.. ... ... ..T ... GA. ... ... C.. ... GA. ... ... ... ... ... ... ... ... ... A.. ... ... ... ... G.. ... A.. ... ... ... ... A.C ... ... ... ... ... ... A.. G.. C.. ... ... ... .AC .A. ... A.. ..C ... A.. ... ... Mmu_rhesus ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... G.. ... AA. ..T ... .A. ... ... C.. ... CA. ... ... ... ... ... ... .A. ... ... A.. ... ... ... ... ... ... A.. ... ... .A. ... ... ... ... ... ... A.. ... A.. ... ... ... ... ... .AC ... ... A.. ... ... ... ... ... Ssc_squirrelM ... ... ..C ... ... ... ... ... ... ... ... ... ... ..G C.T ... ... ... ... ... ... ... ... ... ... ... ... ... ... .AC ..T ... ..T ... ... C.. ... CA. ... ... ... ... ... ... .A. ..T ... A.. .G. ... ... ... ... ... A.. ... ... .A. ... ... G.. A.. C.A ..G ..C ... ... ... ... ... .A. GC. .A. ... ... A.. ... ... ... ... ..A Cja_marmoset ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ..T ... C.. ... ... ... ... ... ... ... ... ... ... ... ... .A. ..T ... ..T ... ... C.. ... CA. ... ... ... ... ... ... .A. ..T ..C A.. .G. ... ... ... ... ... A.. ... ... .A. ... ... G.. A.. ..A ..G ..C ... ..C ... ..G ... .A. GC. .A. ... ... A.. ... ... ... ... ..A Codon usage in sequences -------------------------------------------------------------------------------------------------------------- Phe TTT 2 2 2 2 2 1 | Ser TCT 0 0 0 0 0 0 | Tyr TAT 2 3 3 2 3 4 | Cys TGT 7 7 7 7 7 7 TTC 0 0 0 0 0 1 | TCC 1 1 1 1 1 1 | TAC 4 3 3 4 3 2 | TGC 1 1 1 1 1 1 Leu TTA 1 1 0 0 0 0 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 TTG 4 4 4 4 4 3 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 5 5 5 5 5 5 -------------------------------------------------------------------------------------------------------------- Leu CTT 0 0 0 0 0 1 | Pro CCT 0 1 1 1 1 1 | His CAT 1 1 1 1 1 2 | Arg CGT 3 2 0 0 0 2 CTC 0 1 0 0 0 0 | CCC 0 0 0 0 0 0 | CAC 0 0 1 1 2 1 | CGC 1 2 1 1 0 0 CTA 1 1 1 1 1 1 | CCA 2 2 2 2 2 2 | Gln CAA 4 4 3 3 6 6 | CGA 1 1 1 1 0 0 CTG 2 2 3 3 3 2 | CCG 0 0 0 0 0 0 | CAG 2 2 2 2 2 2 | CGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------- Ile ATT 1 2 1 0 1 1 | Thr ACT 2 2 2 2 3 3 | Asn AAT 5 6 7 5 8 6 | Ser AGT 2 1 3 4 3 2 ATC 3 3 3 3 4 3 | ACC 1 1 1 1 1 1 | AAC 5 5 5 6 5 4 | AGC 3 3 3 3 3 3 ATA 1 1 2 2 2 2 | ACA 2 2 2 2 2 2 | Lys AAA 3 3 5 6 3 3 | Arg AGA 6 6 2 2 5 4 Met ATG 2 2 0 0 0 2 | ACG 0 0 0 0 0 0 | AAG 2 2 4 3 2 2 | AGG 3 3 2 2 3 4 -------------------------------------------------------------------------------------------------------------- Val GTT 3 2 3 4 3 3 | Ala GCT 6 4 5 5 4 4 | Asp GAT 7 7 6 6 6 5 | Gly GGT 2 2 2 2 1 1 GTC 3 2 3 3 2 3 | GCC 3 4 3 3 3 4 | GAC 1 1 1 1 1 3 | GGC 3 3 3 3 3 3 GTA 1 2 2 1 1 1 | GCA 5 5 5 5 5 5 | Glu GAA 1 1 3 3 1 1 | GGA 5 5 5 5 5 5 GTG 2 1 2 3 3 2 | GCG 0 0 0 0 0 0 | GAG 2 2 2 2 2 2 | GGG 1 1 1 1 1 1 -------------------------------------------------------------------------------------------------------------- -------------------------------------------------- Phe TTT 3 | Ser TCT 0 | Tyr TAT 4 | Cys TGT 7 TTC 0 | TCC 1 | TAC 2 | TGC 1 Leu TTA 0 | TCA 0 | *** TAA 0 | *** TGA 0 TTG 3 | TCG 0 | TAG 0 | Trp TGG 5 -------------------------------------------------- Leu CTT 0 | Pro CCT 1 | His CAT 2 | Arg CGT 1 CTC 0 | CCC 0 | CAC 1 | CGC 1 CTA 1 | CCA 2 | Gln CAA 5 | CGA 0 CTG 3 | CCG 0 | CAG 2 | CGG 0 -------------------------------------------------- Ile ATT 1 | Thr ACT 3 | Asn AAT 5 | Ser AGT 2 ATC 3 | ACC 1 | AAC 5 | AGC 3 ATA 2 | ACA 2 | Lys AAA 3 | Arg AGA 3 Met ATG 1 | ACG 0 | AAG 2 | AGG 5 -------------------------------------------------- Val GTT 3 | Ala GCT 4 | Asp GAT 6 | Gly GGT 1 GTC 3 | GCC 4 | GAC 2 | GGC 3 GTA 1 | GCA 5 | Glu GAA 2 | GGA 5 GTG 2 | GCG 0 | GAG 2 | GGG 1 -------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: Hsa_Human position 1: T:0.20769 C:0.13077 A:0.31538 G:0.34615 position 2: T:0.20000 C:0.16923 A:0.30000 G:0.33077 position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231 #2: Hla_gibbon position 1: T:0.20769 C:0.14615 A:0.32308 G:0.32308 position 2: T:0.20000 C:0.16923 A:0.30769 G:0.32308 position 3: T:0.32308 C:0.23077 A:0.26154 G:0.18462 #3: Cgu/Can_colobus position 1: T:0.20000 C:0.12308 A:0.32308 G:0.35385 position 2: T:0.20000 C:0.16923 A:0.35385 G:0.27692 position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231 #4: Pne_langur position 1: T:0.20000 C:0.12308 A:0.31538 G:0.36154 position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462 position 3: T:0.31538 C:0.23846 A:0.25385 G:0.19231 #5: Mmu_rhesus position 1: T:0.20000 C:0.13846 A:0.34615 G:0.31538 position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462 position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231 #6: Ssc_squirrelM position 1: T:0.19231 C:0.15385 A:0.32308 G:0.33077 position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231 position 3: T:0.33077 C:0.23077 A:0.24615 G:0.19231 #7: Cja_marmoset position 1: T:0.20000 C:0.14615 A:0.31538 G:0.33846 position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231 position 3: T:0.33077 C:0.23077 A:0.23846 G:0.20000 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 14 | Ser S TCT 0 | Tyr Y TAT 21 | Cys C TGT 49 TTC 1 | TCC 7 | TAC 21 | TGC 7 Leu L TTA 2 | TCA 0 | *** * TAA 0 | *** * TGA 0 TTG 26 | TCG 0 | TAG 0 | Trp W TGG 35 ------------------------------------------------------------------------------ Leu L CTT 1 | Pro P CCT 6 | His H CAT 9 | Arg R CGT 8 CTC 1 | CCC 0 | CAC 6 | CGC 6 CTA 7 | CCA 14 | Gln Q CAA 31 | CGA 4 CTG 18 | CCG 0 | CAG 14 | CGG 0 ------------------------------------------------------------------------------ Ile I ATT 7 | Thr T ACT 17 | Asn N AAT 42 | Ser S AGT 17 ATC 22 | ACC 7 | AAC 35 | AGC 21 ATA 12 | ACA 14 | Lys K AAA 26 | Arg R AGA 28 Met M ATG 7 | ACG 0 | AAG 17 | AGG 22 ------------------------------------------------------------------------------ Val V GTT 21 | Ala A GCT 32 | Asp D GAT 43 | Gly G GGT 11 GTC 19 | GCC 24 | GAC 10 | GGC 21 GTA 9 | GCA 35 | Glu E GAA 12 | GGA 35 GTG 15 | GCG 0 | GAG 14 | GGG 7 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.20110 C:0.13736 A:0.32308 G:0.33846 position 2: T:0.20000 C:0.17143 A:0.33077 G:0.29780 position 3: T:0.32747 C:0.22857 A:0.25165 G:0.19231 Codon frequencies under model, for use in evolver: 0.01378574 0.00962226 0.01059374 0.00809565 0.01181635 0.00824765 0.00908035 0.00693913 0.02279949 0.01591374 0.00000000 0.00000000 0.02052711 0.01432765 0.00000000 0.01205451 0.00941649 0.00657258 0.00723616 0.00552982 0.00807127 0.00563364 0.00620242 0.00473984 0.01557342 0.01087004 0.01196749 0.00914546 0.01402125 0.00978665 0.01077472 0.00823396 0.02214758 0.01545871 0.01701945 0.01300613 0.01898364 0.01325032 0.01458810 0.01114811 0.03662868 0.02556633 0.02814755 0.02151013 0.03297798 0.02301819 0.02534214 0.01936627 0.02320222 0.01619484 0.01782990 0.01362547 0.01988762 0.01388129 0.01528277 0.01167897 0.03837291 0.02678377 0.02948791 0.02253443 0.03454836 0.02411429 0.02654891 0.02028847 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) Hsa_Human Hla_gibbon 0.2782 (0.0133 0.0478) Cgu/Can_colobus 1.1086 (0.0742 0.0670) 1.1055 (0.0742 0.0671) Pne_langur 1.1979 (0.0725 0.0605) 0.9234 (0.0797 0.0863) 0.5517 (0.0267 0.0484) Mmu_rhesus 1.8744 (0.0562 0.0300) 1.0215 (0.0561 0.0550) 1.2973 (0.0473 0.0364) 1.3970 (0.0508 0.0364) Ssc_squirrelM 0.4701 (0.0633 0.1346) 0.4688 (0.0633 0.1349) 0.5159 (0.0775 0.1502) 0.5833 (0.0959 0.1645) 0.4544 (0.0559 0.1230) Cja_marmoset 0.4725 (0.0634 0.1341) 0.5925 (0.0633 0.1069) 0.4702 (0.0704 0.1496) 0.5411 (0.0886 0.1638) 0.3995 (0.0490 0.1225) 0.1595 (0.0099 0.0619) TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 lnL(ntime: 11 np: 14): -904.636553 +0.000000 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7 0.07000 0.02557 0.03893 0.04388 0.07904 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56118 0.68580 3.50575 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 0.55906 ((1: 0.025570, 2: 0.038929): 0.070000, ((3: 0.043878, 4: 0.052151): 0.079045, 5: 0.019487): 0.043879, (6: 0.041033, 7: 0.023779): 0.121307); ((Hsa_Human: 0.025570, Hla_gibbon: 0.038929): 0.070000, ((Cgu/Can_colobus: 0.043878, Pne_langur: 0.052151): 0.079045, Mmu_rhesus: 0.019487): 0.043879, (Ssc_squirrelM: 0.041033, Cja_marmoset: 0.023779): 0.121307); Detailed output identifying parameters kappa (ts/tv) = 4.56118 dN & dS for each branch branch t S N dN/dS dN dS S*dS N*dN 8..9 0.070 107.8 282.2 0.6858 0.0207 0.0302 3.3 5.8 9..1 0.026 107.8 282.2 0.6858 0.0076 0.0110 1.2 2.1 9..2 0.039 107.8 282.2 0.6858 0.0115 0.0168 1.8 3.2 8..10 0.044 107.8 282.2 0.6858 0.0130 0.0189 2.0 3.7 10..11 0.079 107.8 282.2 3.5057 0.0328 0.0094 1.0 9.3 11..3 0.044 107.8 282.2 0.6858 0.0130 0.0189 2.0 3.7 11..4 0.052 107.8 282.2 0.6858 0.0154 0.0225 2.4 4.4 10..5 0.019 107.8 282.2 0.6858 0.0058 0.0084 0.9 1.6 8..12 0.121 107.8 282.2 0.6858 0.0359 0.0523 5.6 10.1 12..6 0.041 107.8 282.2 0.6858 0.0121 0.0177 1.9 3.4 12..7 0.024 107.8 282.2 0.6858 0.0070 0.0103 1.1 2.0 tree length for dN: 0.17485 tree length for dS: 0.21644 dS tree: ((Hsa_Human: 0.011031, Hla_gibbon: 0.016794): 0.030198, ((Cgu/Can_colobus: 0.018929, Pne_langur: 0.022498): 0.009367, Mmu_rhesus: 0.008407): 0.018929, (Ssc_squirrelM: 0.017702, Cja_marmoset: 0.010258): 0.052332); dN tree: ((Hsa_Human: 0.007565, Hla_gibbon: 0.011517): 0.020710, ((Cgu/Can_colobus: 0.012982, Pne_langur: 0.015429): 0.032838, Mmu_rhesus: 0.005765): 0.012982, (Ssc_squirrelM: 0.012140, Cja_marmoset: 0.007035): 0.035889); TREE # 2: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 lnL(ntime: 11 np: 14): -904.636553 -0.000000 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7 0.07000 0.02557 0.03893 0.04388 0.07905 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56122 0.68581 3.50574 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 0.55906 ((1: 0.025570, 2: 0.038929): 0.070001, ((3: 0.043878, 4: 0.052150): 0.079045, 5: 0.019488): 0.043879, (6: 0.041033, 7: 0.023779): 0.121307); ((Hsa_Human: 0.025570, Hla_gibbon: 0.038929): 0.070001, ((Cgu/Can_colobus: 0.043878, Pne_langur: 0.052150): 0.079045, Mmu_rhesus: 0.019488): 0.043879, (Ssc_squirrelM: 0.041033, Cja_marmoset: 0.023779): 0.121307); Detailed output identifying parameters kappa (ts/tv) = 4.56122 dN & dS for each branch branch t S N dN/dS dN dS S*dS N*dN 8..9 0.070 107.8 282.2 0.6858 0.0207 0.0302 3.3 5.8 9..1 0.026 107.8 282.2 0.6858 0.0076 0.0110 1.2 2.1 9..2 0.039 107.8 282.2 0.6858 0.0115 0.0168 1.8 3.2 8..10 0.044 107.8 282.2 0.6858 0.0130 0.0189 2.0 3.7 10..11 0.079 107.8 282.2 3.5057 0.0328 0.0094 1.0 9.3 11..3 0.044 107.8 282.2 0.6858 0.0130 0.0189 2.0 3.7 11..4 0.052 107.8 282.2 0.6858 0.0154 0.0225 2.4 4.4 10..5 0.019 107.8 282.2 0.6858 0.0058 0.0084 0.9 1.6 8..12 0.121 107.8 282.2 0.6858 0.0359 0.0523 5.6 10.1 12..6 0.041 107.8 282.2 0.6858 0.0121 0.0177 1.9 3.4 12..7 0.024 107.8 282.2 0.6858 0.0070 0.0103 1.1 2.0 tree length for dN: 0.17485 tree length for dS: 0.21644 dS tree: ((Hsa_Human: 0.011031, Hla_gibbon: 0.016794): 0.030198, ((Cgu/Can_colobus: 0.018929, Pne_langur: 0.022497): 0.009367, Mmu_rhesus: 0.008407): 0.018929, (Ssc_squirrelM: 0.017702, Cja_marmoset: 0.010258): 0.052331); dN tree: ((Hsa_Human: 0.007565, Hla_gibbon: 0.011517): 0.020710, ((Cgu/Can_colobus: 0.012982, Pne_langur: 0.015429): 0.032838, Mmu_rhesus: 0.005766): 0.012982, (Ssc_squirrelM: 0.012140, Cja_marmoset: 0.007035): 0.035889); Tree comparisons (Kishino & Hasegawa 1989; Shimodaira & Hasegawa 1999) Number of replicates: 10000 tree li Dli +- SE pKH pSH pRELL 1* -904.637 0.000 0.000 -1.000 -1.000 0.511 2 -904.637 -0.000 0.000 0.500 0.516 0.489 pKH: P value for KH normal test (Kishino & Hasegawa 1989) pRELL: RELL bootstrap proportions (Kishino & Hasegawa 1989) pSH: P value with multiple-comparison correction (MC in table 1 of Shimodaira & Hasegawa 1999) (-1 for P values means N/A) Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml_lysozyme/4fold.nuc0000644000175000017500000000101313316145226024260 0ustar carandraugcarandraug 7 38 Hsa_Human CTGACAAACATAATGCCAAATCCTGTAATCACAGATAG Hla_gibbon CTGACAAACATAATGCCAAATCCTGTAATCACAGATAA Cgu/Can_colobus CTGACAAACATAATGCCAAATCCTGTAATCACAGATAA Pne_langur CTGACAAACATAATGCCAAATCCTGTAATCACAGATAG Mmu_rhesus CTGACAAACATAATGCCAAATCCTGTAATCACAGATAG Ssc_squirrelM CTGACAAACATAATGCCAAATCCTGTGATCACAGATAA Cja_marmoset CTGACAAACATAATGCCAAATCCTGTGATCACAGATAA codons included 9 11 12 16 19 22 25 26 32 40 42 43 48 52 55 68 70 71 72 73 74 76 80 83 85 92 93 96 99 100 103 105 108 110 111 127 129 130 Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml_lysozyme/rst10000644000175000017500000000007213316145226023361 0ustar carandraugcarandraug 1 -0.00 0.511 0.489 -1.000 0.52 0.00 Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml_lysozyme/lysozymeSmall.ctl0000644000175000017500000000337413316145226026145 0ustar carandraugcarandraug seqfile = lysozymeSmall.txt treefile = lysozymeSmall.trees outfile = mlc noisy = 9 * 0,1,2,3,9: how much rubbish on the screen verbose = 1 * 1: detailed output, 0: concise output runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic * 3: StepwiseAddition; (4,5):PerturbationNNI seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table model = 2 * models for codons: * 0:one, 1:b, 2:2 or more dN/dS ratios for branches NSsites = 0 * dN/dS among sites. 0:no variation, 1:neutral, 2:positive icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated kappa = 2 * initial or fixed kappa fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate omega = 1 * initial or fixed omega, for codons or codon-transltd AAs fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha alpha = .0 * initial or fixed alpha, 0:infinity (constant rate) Malpha = 0 * different alphas for genes ncatG = 4 * # of categories in the dG or AdG models of rates clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree getSE = 0 * 0: don't want them, 1: want S.E.s of estimates RateAncestor = 1 * (1/0): rates (alpha>0) or ancestral states (alpha=0) method = 0 * 0: simultaneous; 1: one branch at a time * Specifications for duplicating results for the small data set in table 1 * of Yang (1998 MBE 15:568-573). * see the tree file lysozyme.trees for specification of node (branch) labels Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml_lysozyme/lysozymeSmall.txt0000644000175000017500000000566413316145226026206 0ustar carandraugcarandraug 7 390 Hsa_Human AAGGTCTTTGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAGATTGGGAATGGATGGCTAC AGGGGAATCAGCCTAGCAAACTGGATGTGTTTGGCCAAATGGGAGAGTGGTTACAACACA CGAGCTACAAACTACAATGCTGGAGACAGAAGCACTGATTATGGGATATTTCAGATCAAT AGCCGCTACTGGTGTAATGATGGCAAAACCCCAGGAGCAGTTAATGCCTGTCATTTATCC TGCAGTGCTTTGCTGCAAGATAACATCGCTGATGCTGTAGCTTGTGCAAAGAGGGTTGTC CGTGATCCACAAGGCATTAGAGCATGGGTGGCATGGAGAAATCGTTGTCAAAACAGAGAT GTCCGTCAGTATGTTCAAGGTTGTGGAGTG Hla_gibbon AAGGTCTTTGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAGATTGGGAATGGATGGCTAC AGGGGAATCAGCCTAGCAAACTGGATGTGTTTGGCCAAATGGGAGAGTGGTTATAACACA CGAGCTACAAACTACAATCCTGGAGACAGAAGCACTGATTATGGGATATTTCAGATCAAT AGCCGCTACTGGTGTAATGATGGCAAAACCCCAGGAGCAGTTAATGCCTGTCATTTATCC TGCAATGCTTTGCTGCAAGATAACATCGCCGATGCTGTAGCTTGTGCAAAGAGGGTTGTC CGCGATCCACAAGGCATTAGAGCATGGGTGGCATGGAGAAATCGTTGTCAAAACAGAGAT CTCCGTCAGTATATTCAAGGTTGTGGAGTA Cgu/Can_colobus AAGATCTTTGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAAATTGGGACTGGATGGCTAC AAGGGAGTCAGCCTAGCAAACTGGGTGTGTTTGGCCAAATGGGAGAGTGGTTATAACACA GACGCTACAAACTACAATCCTGGAGATGAAAGCACTGATTATGGGATATTTCAGATCAAT AGCCGCTACTGGTGTAATAATGGCAAAACCCCAGGAGCAGTTAATGCCTGTCATATATCC TGCAATGCTTTGCTGCAAAATAACATCGCTGATGCTGTAGCTTGTGCAAAGAGGGTTGTC AGTGATCCACAAGGCATTCGAGCATGGGTGGCATGGAAAAAGCACTGTCAAAACAGAGAT GTCAGTCAGTATGTTGAAGGTTGTGGAGTA Pne_langur AAGATCTTTGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAAATTGGGACTGGATGGCTAC AAGGGAGTCAGCCTAGCAAACTGGGTGTGTTTGGCCAAATGGGAGAGTGGTTATAACACA GAAGCTACAAACTACAATCCTGGAGACGAAAGCACTGATTATGGGATATTTCAGATCAAT AGCCGCTACTGGTGTAATAATGGCAAAACCCCAGGAGCAGTTGATGCCTGTCATATATCC TGCAGTGCTTTGCTGCAAAACAACATCGCTGATGCTGTAGCTTGTGCAAAGAGGGTTGTC AGTGATCCACAAGGCGTTCGAGCATGGGTGGCATGGAGAAATCACTGTCAAAACAAAGAT GTCAGTCAGTACGTTAAAGGTTGTGGAGTG Mmu_rhesus AAGATCTTTGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAGATTGGGACTGGATGGCTAC AGGGGAATCAGCCTAGCAAACTGGGTGTGTTTGGCCAAATGGGAGAGTAATTATAACACA CAAGCTACAAACTACAATCCTGGAGACCAAAGCACTGATTATGGGATATTTCAGATCAAT AGCCACTACTGGTGTAATAATGGCAAAACCCCAGGAGCAGTTAATGCCTGTCATATATCC TGCAATGCTTTGCTGCAAGATAACATCGCTGATGCTGTAACTTGTGCAAAGAGGGTTGTC AGTGATCCACAAGGCATTAGAGCATGGGTGGCATGGAGAAATCACTGTCAAAACAGAGAT GTCAGTCAGTATGTTCAAGGTTGTGGAGTG Ssc_squirrelM AAGGTCTTCGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAGGCTTGGAATGGATGGCTAC AGGGGAATCAGCCTAGCAAACTGGATGTGTTTGGCCAAATGGGAGAGTGACTATAACACA CGTGCTACAAACTACAATCCTGGAGACCAAAGCACTGATTATGGGATATTTCAGATCAAT AGCCACTATTGGTGTAATAATGGCAGAACCCCAGGAGCAGTTAATGCCTGTCATATATCC TGCAATGCTTTGCTGCAAGATGACATCACTCAAGCTGTGGCCTGTGCAAAGAGGGTTGTC CGTGATCCACAAGGCATTAGAGCATGGGTGGCATGGAAAGCTCATTGTCAAAACAGAGAT GTCAGTCAGTATGTTCAAGGTTGTGGAGTA Cja_marmoset AAGGTCTTTGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAGGTTTGGACTGGATGGCTAC AGGGGAATCAGCCTAGCAAACTGGATGTGTTTGGCCAAATGGGAGAGTGATTATAACACA CGTGCTACAAACTACAATCCTGGAGACCAAAGCACTGATTATGGGATATTTCAGATCAAT AGCCACTATTGGTGTAACAATGGCAGAACCCCAGGAGCAGTTAATGCCTGTCATATATCC TGCAATGCTTTGCTGCAAGATGACATCACTGAAGCTGTGGCCTGTGCAAAGAGGGTTGTC CGCGATCCACAAGGCATTAGGGCATGGGTGGCATGGAAAGCTCATTGTCAAAACAGAGAT GTCAGTCAGTATGTTCAAGGTTGTGGAGTA Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml_lysozyme/rst0000644000175000017500000034072613316145226023315 0ustar carandraugcarandraugSupplemental results for CODEML (seqf: lysozymeSmall.txt treef: lysozymeSmall.trees) Number of codon sites with 0,1,2,3 position differences 2 vs. 1 122 8 0 0 0.2782 (0.0133 0.0478) 3 vs. 1 107 20 2 1 1.1086 (0.0742 0.0670) 3 vs. 2 108 18 3 1 1.1055 (0.0742 0.0671) 4 vs. 1 108 18 4 0 1.1979 (0.0725 0.0605) 4 vs. 2 105 20 5 0 0.9234 (0.0797 0.0863) 4 vs. 3 118 12 0 0 0.5517 (0.0267 0.0484) 5 vs. 1 114 13 3 0 1.8744 (0.0562 0.0300) 5 vs. 2 113 13 4 0 1.0215 (0.0561 0.0550) 5 vs. 3 115 13 2 0 1.2973 (0.0473 0.0364) 5 vs. 4 114 14 2 0 1.3970 (0.0508 0.0364) 6 vs. 1 106 19 5 0 0.4701 (0.0633 0.1346) 6 vs. 2 107 17 6 0 0.4688 (0.0633 0.1349) 6 vs. 3 104 20 4 2 0.5159 (0.0775 0.1502) 6 vs. 4 98 25 6 1 0.5833 (0.0959 0.1645) 6 vs. 5 110 14 6 0 0.4544 (0.0559 0.1230) 7 vs. 1 103 25 2 0 0.4725 (0.0634 0.1341) 7 vs. 2 106 21 3 0 0.5925 (0.0633 0.1069) 7 vs. 3 105 20 3 2 0.4702 (0.0704 0.1496) 7 vs. 4 99 25 5 1 0.5411 (0.0886 0.1638) 7 vs. 5 110 16 4 0 0.3995 (0.0490 0.1225) 7 vs. 6 122 8 0 0 0.1595 (0.0099 0.0619) TREE # 1 Ancestral reconstruction by CODONML. ((Hsa_Human: 0.007565, Hla_gibbon: 0.011517): 0.020710, ((Cgu/Can_colobus: 0.012982, Pne_langur: 0.015429): 0.032838, Mmu_rhesus: 0.005765): 0.012982, (Ssc_squirrelM: 0.012140, Cja_marmoset: 0.007035): 0.035889); ((1, 2), ((3, 4), 5), (6, 7)); 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7 tree with node labels for Rod Page's TreeView ((1_Hsa_Human: 0.007565, 2_Hla_gibbon: 0.011517) 9 : 0.020710, ((3_Cgu/Can_colobus: 0.012982, 4_Pne_langur: 0.015429) 11 : 0.032838, 5_Mmu_rhesus: 0.005765) 10 : 0.012982, (6_Ssc_squirrelM: 0.012140, 7_Cja_marmoset: 0.007035) 12 : 0.035889) 8 ; Nodes 8 to 12 are ancestral (1) Marginal reconstruction of ancestral sequences (eqn. 4 in Yang et al. 1995 Genetics 141:1641-1650). Prob of best character at each node, listed by site Site Freq Data: 1 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) 2 1 GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) GTC (V) GTC (V) : GTC V 0.967 (V 0.967) GTC V 1.000 (V 1.000) ATC I 0.992 (I 0.992) ATC I 1.000 (I 1.000) GTC V 1.000 (V 1.000) 3 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTC (F) TTT (F) : TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 0.985 (F 1.000) 4 1 GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) : GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) 5 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) 6 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) 7 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) 8 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) 9 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) 10 1 AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) : AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) 11 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) 12 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) 13 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) 14 1 AGA (R) AGA (R) AAA (K) AAA (K) AGA (R) AGG (R) AGG (R) : AGA R 0.990 (R 1.000) AGA R 1.000 (R 1.000) AGA R 0.998 (R 0.998) AAA K 0.994 (K 0.994) AGG R 0.998 (R 1.000) 15 1 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) CTT (L) TTT (F) : TTG L 0.999 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTT F 0.990 (F 0.990) 16 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) 17 1 ATG (M) ATG (M) CTG (L) CTG (L) CTG (L) ATG (M) CTG (L) : CTG L 0.871 (L 0.871) ATG M 1.000 (M 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 0.871 (L 0.871) 18 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) 19 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) 20 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) 21 1 AGG (R) AGG (R) AAG (K) AAG (K) AGG (R) AGG (R) AGG (R) : AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 0.998 (R 0.998) AAG K 0.995 (K 0.995) AGG R 1.000 (R 1.000) 22 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) 23 1 ATC (I) ATC (I) GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) : ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 0.999 (I 0.999) GTC V 0.996 (V 0.996) ATC I 1.000 (I 1.000) 24 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) 25 1 CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) : CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) 26 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) 27 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) 28 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) 29 1 ATG (M) ATG (M) GTG (V) GTG (V) GTG (V) ATG (M) ATG (M) : ATG M 0.974 (M 0.974) ATG M 1.000 (M 1.000) GTG V 0.993 (V 0.993) GTG V 1.000 (V 1.000) ATG M 1.000 (M 1.000) 30 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) 31 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) 32 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) 33 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) 34 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) 35 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) 36 1 AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) 37 1 GGT (G) GGT (G) GGT (G) GGT (G) AAT (N) GAC (D) GAT (D) : GAT D 0.742 (D 0.743) GGT G 0.996 (G 0.996) GAT D 0.696 (D 0.696) GGT G 0.993 (G 0.993) GAT D 0.959 (D 0.999) 38 1 TAC (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT Y 0.999 (Y 1.000) TAT Y 0.962 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) 39 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) 40 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) 41 1 CGA (R) CGA (R) GAC (D) GAA (E) CAA (Q) CGT (R) CGT (R) : CGA R 0.977 (R 0.978) CGA R 1.000 (R 1.000) CAA Q 0.990 (Q 0.990) GAA E 0.992 (E 0.992) CGT R 1.000 (R 1.000) 42 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) 43 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) 44 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) 45 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) 46 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) 47 1 GCT (A) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) : CCT P 1.000 (P 1.000) CCT P 0.998 (P 0.998) CCT P 1.000 (P 1.000) CCT P 1.000 (P 1.000) CCT P 1.000 (P 1.000) 48 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) 49 1 GAC (D) GAC (D) GAT (D) GAC (D) GAC (D) GAC (D) GAC (D) : GAC D 1.000 (D 1.000) GAC D 1.000 (D 1.000) GAC D 1.000 (D 1.000) GAC D 0.989 (D 1.000) GAC D 1.000 (D 1.000) 50 1 AGA (R) AGA (R) GAA (E) GAA (E) CAA (Q) CAA (Q) CAA (Q) : CAA Q 0.980 (Q 0.980) AGA R 0.994 (R 0.995) CAA Q 0.990 (Q 0.990) GAA E 0.998 (E 0.998) CAA Q 1.000 (Q 1.000) 51 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) 52 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) 53 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) 54 1 TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) 55 1 GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) : GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) 56 1 ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) 57 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) : TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) 58 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) 59 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) 60 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) 61 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) 62 1 CGC (R) CGC (R) CGC (R) CGC (R) CAC (H) CAC (H) CAC (H) : CAC H 0.742 (H 0.742) CGC R 0.999 (R 0.999) CAC H 0.748 (H 0.748) CGC R 0.998 (R 0.998) CAC H 1.000 (H 1.000) 63 1 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAT (Y) TAT (Y) : TAC Y 0.994 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAT Y 0.997 (Y 1.000) 64 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) 65 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) 66 1 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAC (N) : AAT N 0.998 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 0.889 (N 1.000) 67 1 GAT (D) GAT (D) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT N 0.970 (N 0.970) GAT D 0.994 (D 0.994) AAT N 0.999 (N 0.999) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) 68 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) 69 1 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AGA (R) AGA (R) : AAA K 0.992 (K 0.992) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AGA R 0.998 (R 0.998) 70 1 ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) : ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) 71 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) 72 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) 73 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) 74 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) 75 1 AAT (N) AAT (N) AAT (N) GAT (D) AAT (N) AAT (N) AAT (N) : AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 0.964 (N 0.964) AAT N 1.000 (N 1.000) 76 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) 77 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) 78 1 CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) : CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) 79 1 TTA (L) TTA (L) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA I 0.997 (I 0.997) TTA L 1.000 (L 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) 80 1 TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) : TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) 81 1 TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) : TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) 82 1 AGT (S) AAT (N) AAT (N) AGT (S) AAT (N) AAT (N) AAT (N) : AAT N 0.998 (N 0.998) AAT N 0.957 (N 0.957) AAT N 0.999 (N 0.999) AAT N 0.963 (N 0.963) AAT N 1.000 (N 1.000) 83 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) 84 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) 85 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) 86 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) 87 1 GAT (D) GAT (D) AAT (N) AAC (N) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 0.996 (D 0.997) AAT N 0.983 (N 0.993) GAT D 1.000 (D 1.000) 88 1 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) GAC (D) GAC (D) : AAC N 0.993 (N 0.993) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) GAC D 0.998 (D 0.998) 89 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) 90 1 GCT (A) GCC (A) GCT (A) GCT (A) GCT (A) ACT (T) ACT (T) : GCT A 0.994 (A 0.994) GCT A 0.985 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) ACT T 0.998 (T 0.998) 91 1 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) CAA (Q) GAA (E) : GAT D 0.997 (D 0.997) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAA E 0.995 (E 0.995) 92 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) 93 1 GTA (V) GTA (V) GTA (V) GTA (V) GTA (V) GTG (V) GTG (V) : GTA V 0.993 (V 1.000) GTA V 1.000 (V 1.000) GTA V 1.000 (V 1.000) GTA V 1.000 (V 1.000) GTG V 0.998 (V 1.000) 94 1 GCT (A) GCT (A) GCT (A) GCT (A) ACT (T) GCC (A) GCC (A) : GCT A 0.990 (A 0.998) GCT A 1.000 (A 1.000) GCT A 0.947 (A 0.947) GCT A 1.000 (A 1.000) GCC A 0.998 (A 1.000) 95 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) 96 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) 97 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) 98 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) 99 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) 100 1 GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) 101 1 CGT (R) CGC (R) AGT (S) AGT (S) AGT (S) CGT (R) CGC (R) : CGT R 0.973 (R 0.993) CGT R 0.970 (R 1.000) AGT S 0.995 (S 0.996) AGT S 1.000 (S 1.000) CGT R 0.935 (R 1.000) 102 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) 103 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) 104 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) 105 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) 106 1 ATT (I) ATT (I) ATT (I) GTT (V) ATT (I) ATT (I) ATT (I) : ATT I 1.000 (I 1.000) ATT I 1.000 (I 1.000) ATT I 1.000 (I 1.000) ATT I 0.978 (I 0.978) ATT I 1.000 (I 1.000) 107 1 AGA (R) AGA (R) CGA (R) CGA (R) AGA (R) AGA (R) AGG (R) : AGA R 0.999 (R 1.000) AGA R 1.000 (R 1.000) AGA R 0.996 (R 1.000) CGA R 0.996 (R 1.000) AGA R 0.921 (R 1.000) 108 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) 109 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) 110 1 GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) : GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) 111 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) 112 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) 113 1 AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AAA (K) AAA (K) : AGA R 0.990 (R 0.990) AGA R 1.000 (R 1.000) AGA R 0.997 (R 0.997) AGA R 0.962 (R 0.962) AAA K 0.998 (K 0.998) 114 1 AAT (N) AAT (N) AAG (K) AAT (N) AAT (N) GCT (A) GCT (A) : AAT N 0.984 (N 0.984) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 0.987 (N 0.988) GCT A 0.998 (A 0.998) 115 1 CGT (R) CGT (R) CAC (H) CAC (H) CAC (H) CAT (H) CAT (H) : CAT H 0.952 (H 0.990) CGT R 0.998 (R 0.998) CAC H 0.998 (H 1.000) CAC H 1.000 (H 1.000) CAT H 1.000 (H 1.000) 116 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) 117 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) 118 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) 119 1 AGA (R) AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AGA (R) : AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 0.975 (R 0.975) AGA R 1.000 (R 1.000) 120 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) 121 1 GTC (V) CTC (L) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC V 1.000 (V 1.000) GTC V 0.998 (V 0.998) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) 122 1 CGT (R) CGT (R) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT S 0.993 (S 0.993) CGT R 0.999 (R 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) 123 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) 124 1 TAT (Y) TAT (Y) TAT (Y) TAC (Y) TAT (Y) TAT (Y) TAT (Y) : TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 0.993 (Y 1.000) TAT Y 1.000 (Y 1.000) 125 1 GTT (V) ATT (I) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT V 1.000 (V 1.000) GTT V 0.988 (V 0.988) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) 126 1 CAA (Q) CAA (Q) GAA (E) AAA (K) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) GAA E 0.517 (E 0.517) CAA Q 1.000 (Q 1.000) 127 1 GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) : GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) 128 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) 129 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) 130 1 GTG (V) GTA (V) GTA (V) GTG (V) GTG (V) GTA (V) GTA (V) : GTG V 0.797 (V 1.000) GTG V 0.795 (V 1.000) GTG V 0.942 (V 1.000) GTG V 0.937 (V 1.000) GTA V 0.998 (V 1.000) Summary of changes along branches. Check root for directions of change. Branch 1: 8..9 (n= 8.5 s= 0.5) 17 L 0.871 -> M 1.000 37 D 0.743 -> G 0.996 50 Q 0.980 -> R 0.995 62 H 0.742 -> R 0.999 67 N 0.970 -> D 0.994 79 I 0.997 -> L 1.000 115 H 0.990 -> R 0.998 122 S 0.993 -> R 1.000 Branch 2: 9..1 (Hsa_Human) (n= 2.0 s= 1.0) 47 P 0.998 -> A 82 N 0.957 -> S Branch 3: 9..2 (Hla_gibbon) (n= 2.0 s= 3.0) 121 V 0.998 -> L 125 V 0.988 -> I Branch 4: 8..10 (n= 4.0 s= 1.0) 2 V 0.967 -> I 0.992 29 M 0.974 -> V 0.993 41 R 0.978 -> Q 0.990 101 R 0.993 -> S 0.996 Branch 5: 10..11 (n= 9.0 s= 1.0) 14 R 0.998 -> K 0.994 21 R 0.998 -> K 0.995 23 I 0.999 -> V 0.996 37 D 0.696 -> G 0.993 41 Q 0.990 -> E 0.992 50 Q 0.990 -> E 0.998 62 H 0.748 -> R 0.998 87 D 0.997 -> N 0.993 126 Q 1.000 -> E 0.517 Branch 6: 11..3 (Cgu/Can_colobus) (n= 3.0 s= 2.0) 41 E 0.992 -> D 113 R 0.962 -> K 114 N 0.988 -> K Branch 7: 11..4 (Pne_langur) (n= 5.0 s= 2.0) 75 N 0.964 -> D 82 N 0.963 -> S 106 I 0.978 -> V 119 R 0.975 -> K 126 E 0.517 -> K Branch 8: 10..5 (Mmu_rhesus) (n= 2.0 s= 0.0) 37 D 0.696 -> N 94 A 0.947 -> T Branch 9: 8..12 (n= 8.0 s= 6.0) 15 L 1.000 -> F 0.990 69 K 0.992 -> R 0.998 88 N 0.993 -> D 0.998 90 A 0.994 -> T 0.998 91 D 0.997 -> E 0.995 113 R 0.990 -> K 0.998 114 N 0.984 -> A 0.998 Branch 10: 12..6 (Ssc_squirrelM) (n= 3.0 s= 2.0) 15 F 0.990 -> L 17 L 0.871 -> M 91 E 0.995 -> Q Branch 11: 12..7 (Cja_marmoset) (n= 0.0 s= 3.0) List of extant and reconstructed sequences Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAC AAC ACA CGA GCT ACA AAC TAC AAT GCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AGT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG Hla_gibbon AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCC GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT CTC CGT CAG TAT ATT CAA GGT TGT GGA GTA Cgu/Can_colobus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAC GCT ACA AAC TAC AAT CCT GGA GAT GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AAA AAG CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTA Pne_langur AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT GAT GCC TGT CAT ATA TCC TGC AGT GCT TTG CTG CAA AAC AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC GTT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AAA GAT GTC AGT CAG TAC GTT AAA GGT TGT GGA GTG Mmu_rhesus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT AAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA ACT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG Ssc_squirrelM AAG GTC TTC GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG CTT GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAC TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT CAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA Cja_marmoset AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAC AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGG GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA node #8 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG node #9 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG node #10 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG node #11 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTG node #12 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA Overall accuracy of the 5 ancestral sequences: 0.99108 0.99716 0.99439 0.99393 0.99633 for a site. 0.27875 0.67341 0.43633 0.37872 0.60699 for the sequence. Amino acid sequences inferred by codonml. Node #8 KVFERCELAR TLKRLGLDGY RGISLANWMC LAKWESDYNT RATNYNPGDQ STDYGIFQIN SHYWCNNGKT PGAVNACHIS CNALLQDNIA DAVACAKRVV RDPQGIRAWV AWRNHCQNRD VSQYVQGCGV Node #9 KVFERCELAR TLKRLGMDGY RGISLANWMC LAKWESGYNT RATNYNPGDR STDYGIFQIN SRYWCNDGKT PGAVNACHLS CNALLQDNIA DAVACAKRVV RDPQGIRAWV AWRNRCQNRD VRQYVQGCGV Node #10 KIFERCELAR TLKRLGLDGY RGISLANWVC LAKWESDYNT QATNYNPGDQ STDYGIFQIN SHYWCNNGKT PGAVNACHIS CNALLQDNIA DAVACAKRVV SDPQGIRAWV AWRNHCQNRD VSQYVQGCGV Node #11 KIFERCELAR TLKKLGLDGY KGVSLANWVC LAKWESGYNT EATNYNPGDE STDYGIFQIN SRYWCNNGKT PGAVNACHIS CNALLQNNIA DAVACAKRVV SDPQGIRAWV AWRNHCQNRD VSQYVEGCGV Node #12 KVFERCELAR TLKRFGLDGY RGISLANWMC LAKWESDYNT RATNYNPGDQ STDYGIFQIN SHYWCNNGRT PGAVNACHIS CNALLQDDIT EAVACAKRVV RDPQGIRAWV AWKAHCQNRD VSQYVQGCGV Changes at sites (syn nonsyn). 1 (0.0 0.0) 2 GTC.ATC (0.0 1.0) 3 TTT.TTC (1.0 0.0) 4 (0.0 0.0) 5 (0.0 0.0) 6 (0.0 0.0) 7 (0.0 0.0) 8 (0.0 0.0) 9 (0.0 0.0) 10 (0.0 0.0) 11 (0.0 0.0) 12 (0.0 0.0) 13 (0.0 0.0) 14 AGA.AAA AGA.AGG (1.0 1.0) 15 TTT.CTT TTG.TTT (0.0 2.0) 16 (0.0 0.0) 17 CTG.ATG CTG.ATG (0.0 2.0) 18 (0.0 0.0) 19 (0.0 0.0) 20 (0.0 0.0) 21 AGG.AAG (0.0 1.0) 22 (0.0 0.0) 23 ATC.GTC (0.0 1.0) 24 (0.0 0.0) 25 (0.0 0.0) 26 (0.0 0.0) 27 (0.0 0.0) 28 (0.0 0.0) 29 ATG.GTG (0.0 1.0) 30 (0.0 0.0) 31 (0.0 0.0) 32 (0.0 0.0) 33 (0.0 0.0) 34 (0.0 0.0) 35 (0.0 0.0) 36 (0.0 0.0) 37 GAT.AAT GAT.GAC GAT.GGT GAT.GGT (1.0 3.0) 38 TAT.TAC (1.0 0.0) 39 (0.0 0.0) 40 (0.0 0.0) 41 GAA.GAC CGA.CAA CAA.GAA CGA.CGT (1.0 3.0) 42 (0.0 0.0) 43 (0.0 0.0) 44 (0.0 0.0) 45 (0.0 0.0) 46 (0.0 0.0) 47 CCT.GCT (0.0 1.0) 48 (0.0 0.0) 49 GAC.GAT (1.0 0.0) 50 CAA.AGA CAA.GAA (0.5 2.5) 51 (0.0 0.0) 52 (0.0 0.0) 53 (0.0 0.0) 54 (0.0 0.0) 55 (0.0 0.0) 56 (0.0 0.0) 57 (0.0 0.0) 58 (0.0 0.0) 59 (0.0 0.0) 60 (0.0 0.0) 61 (0.0 0.0) 62 CAC.CGC CAC.CGC (0.0 2.0) 63 TAC.TAT (1.0 0.0) 64 (0.0 0.0) 65 (0.0 0.0) 66 AAT.AAC (1.0 0.0) 67 AAT.GAT (0.0 1.0) 68 (0.0 0.0) 69 AAA.AGA (0.0 1.0) 70 (0.0 0.0) 71 (0.0 0.0) 72 (0.0 0.0) 73 (0.0 0.0) 74 (0.0 0.0) 75 AAT.GAT (0.0 1.0) 76 (0.0 0.0) 77 (0.0 0.0) 78 (0.0 0.0) 79 ATA.TTA (0.0 1.0) 80 (0.0 0.0) 81 (0.0 0.0) 82 AAT.AGT AAT.AGT (0.0 2.0) 83 (0.0 0.0) 84 (0.0 0.0) 85 (0.0 0.0) 86 (0.0 0.0) 87 AAT.AAC GAT.AAT (1.0 1.0) 88 AAC.GAC (0.0 1.0) 89 (0.0 0.0) 90 GCT.GCC GCT.ACT (1.0 1.0) 91 GAA.CAA GAT.GAA (0.0 2.0) 92 (0.0 0.0) 93 GTA.GTG (1.0 0.0) 94 GCT.ACT GCT.GCC (1.0 1.0) 95 (0.0 0.0) 96 (0.0 0.0) 97 (0.0 0.0) 98 (0.0 0.0) 99 (0.0 0.0) 100 (0.0 0.0) 101 CGT.CGC CGT.CGC CGT.AGT (2.0 1.0) 102 (0.0 0.0) 103 (0.0 0.0) 104 (0.0 0.0) 105 (0.0 0.0) 106 ATT.GTT (0.0 1.0) 107 AGA.AGG AGA.CGA (2.0 0.0) 108 (0.0 0.0) 109 (0.0 0.0) 110 (0.0 0.0) 111 (0.0 0.0) 112 (0.0 0.0) 113 AGA.AAA AGA.AAA (0.0 2.0) 114 AAT.AAG AAT.GCT (0.0 3.0) 115 CAT.CGT CAT.CAC (1.0 1.0) 116 (0.0 0.0) 117 (0.0 0.0) 118 (0.0 0.0) 119 AGA.AAA (0.0 1.0) 120 (0.0 0.0) 121 GTC.CTC (0.0 1.0) 122 AGT.CGT (0.0 1.0) 123 (0.0 0.0) 124 TAT.TAC (1.0 0.0) 125 GTT.ATT (0.0 1.0) 126 GAA.AAA CAA.GAA (0.0 2.0) 127 (0.0 0.0) 128 (0.0 0.0) 129 (0.0 0.0) 130 GTG.GTA GTG.GTA GTG.GTA (3.0 0.0) (2) Joint reconstruction of ancestral sequences (eqn. 2 in Yang et al. 1995 Genetics 141:1641-1650), using the algorithm of Pupko et al. (2000 Mol Biol Evol 17:890-896). Listed by site, reconstruction (prob.) Site Freq Data: 1 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG AAG AAG AAG AAG (0.9999) 2 1 GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) GTC (V) GTC (V) : GTC GTC ATC ATC GTC (0.9589) 3 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTC (F) TTT (F) : TTT TTT TTT TTT TTT (0.9846) 4 1 GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) : GAA GAA GAA GAA GAA (0.9999) 5 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG AGG AGG AGG AGG (1.0000) 6 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) 7 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG GAG GAG GAG GAG (0.9999) 8 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG TTG TTG TTG TTG (1.0000) 9 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC GCC GCC GCC GCC (1.0000) 10 1 AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) : AGA AGA AGA AGA AGA (0.9999) 11 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT ACT ACT ACT ACT (1.0000) 12 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG CTG CTG CTG CTG (1.0000) 13 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA AAA AAA AAA AAA (0.9999) 14 1 AGA (R) AGA (R) AAA (K) AAA (K) AGA (R) AGG (R) AGG (R) : AGA AGA AGA AAA AGG (0.9789) 15 1 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) CTT (L) TTT (F) : TTG TTG TTG TTG TTT (0.9894) 16 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) 17 1 ATG (M) ATG (M) CTG (L) CTG (L) CTG (L) ATG (M) CTG (L) : CTG ATG CTG CTG CTG (0.8701) 18 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) 19 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC GGC GGC GGC GGC (0.9999) 20 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC TAC TAC TAC TAC (1.0000) 21 1 AGG (R) AGG (R) AAG (K) AAG (K) AGG (R) AGG (R) AGG (R) : AGG AGG AGG AAG AGG (0.9935) 22 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) 23 1 ATC (I) ATC (I) GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) : ATC ATC ATC GTC ATC (0.9950) 24 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC AGC AGC AGC AGC (0.9999) 25 1 CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) : CTA CTA CTA CTA CTA (1.0000) 26 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) 27 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) 28 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) 29 1 ATG (M) ATG (M) GTG (V) GTG (V) GTG (V) ATG (M) ATG (M) : ATG ATG GTG GTG ATG (0.9668) 30 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) 31 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG TTG TTG TTG TTG (1.0000) 32 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC GCC GCC GCC GCC (1.0000) 33 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA AAA AAA AAA AAA (0.9999) 34 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) 35 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG GAG GAG GAG GAG (0.9999) 36 1 AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT AGT AGT AGT AGT (0.9998) 37 1 GGT (G) GGT (G) GGT (G) GGT (G) AAT (N) GAC (D) GAT (D) : GAT GGT GAT GGT GAT (0.6376) 38 1 TAC (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT TAT TAT TAT TAT (0.9616) 39 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) 40 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA ACA ACA ACA ACA (1.0000) 41 1 CGA (R) CGA (R) GAC (D) GAA (E) CAA (Q) CGT (R) CGT (R) : CGA CGA CAA GAA CGT (0.9586) 42 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT GCT GCT GCT GCT (1.0000) 43 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA ACA ACA ACA ACA (1.0000) 44 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) 45 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC TAC TAC TAC TAC (1.0000) 46 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9998) 47 1 GCT (A) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) : CCT CCT CCT CCT CCT (0.9979) 48 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) 49 1 GAC (D) GAC (D) GAT (D) GAC (D) GAC (D) GAC (D) GAC (D) : GAC GAC GAC GAC GAC (0.9890) 50 1 AGA (R) AGA (R) GAA (E) GAA (E) CAA (Q) CAA (Q) CAA (Q) : CAA AGA CAA GAA CAA (0.9726) 51 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC AGC AGC AGC AGC (0.9999) 52 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT ACT ACT ACT ACT (1.0000) 53 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) 54 1 TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT TAT TAT TAT TAT (1.0000) 55 1 GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) : GGG GGG GGG GGG GGG (1.0000) 56 1 ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA ATA ATA ATA ATA (1.0000) 57 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) : TTT TTT TTT TTT TTT (1.0000) 58 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG CAG CAG CAG CAG (1.0000) 59 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC ATC ATC ATC ATC (1.0000) 60 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9998) 61 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC AGC AGC AGC AGC (0.9999) 62 1 CGC (R) CGC (R) CGC (R) CGC (R) CAC (H) CAC (H) CAC (H) : CAC CGC CAC CGC CAC (0.7383) 63 1 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAT (Y) TAT (Y) : TAC TAC TAC TAC TAT (0.9908) 64 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) 65 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) 66 1 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAC (N) : AAT AAT AAT AAT AAT (0.8888) 67 1 GAT (D) GAT (D) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT GAT AAT AAT AAT (0.9642) 68 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC GGC GGC GGC GGC (0.9999) 69 1 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AGA (R) AGA (R) : AAA AAA AAA AAA AGA (0.9899) 70 1 ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) : ACC ACC ACC ACC ACC (1.0000) 71 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA CCA CCA CCA CCA (1.0000) 72 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) 73 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) 74 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT GTT GTT GTT GTT (0.9999) 75 1 AAT (N) AAT (N) AAT (N) GAT (D) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9638) 76 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC GCC GCC GCC GCC (1.0000) 77 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) 78 1 CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) : CAT CAT CAT CAT CAT (1.0000) 79 1 TTA (L) TTA (L) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA TTA ATA ATA ATA (0.9961) 80 1 TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) : TCC TCC TCC TCC TCC (1.0000) 81 1 TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) : TGC TGC TGC TGC TGC (1.0000) 82 1 AGT (S) AAT (N) AAT (N) AGT (S) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9225) 83 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT GCT GCT GCT GCT (1.0000) 84 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG TTG TTG TTG TTG (1.0000) 85 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG CTG CTG CTG CTG (1.0000) 86 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA CAA CAA (1.0000) 87 1 GAT (D) GAT (D) AAT (N) AAC (N) GAT (D) GAT (D) GAT (D) : GAT GAT GAT AAT GAT (0.9799) 88 1 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) GAC (D) GAC (D) : AAC AAC AAC AAC GAC (0.9905) 89 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC ATC ATC ATC ATC (1.0000) 90 1 GCT (A) GCC (A) GCT (A) GCT (A) GCT (A) ACT (T) ACT (T) : GCT GCT GCT GCT ACT (0.9782) 91 1 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) CAA (Q) GAA (E) : GAT GAT GAT GAT GAA (0.9916) 92 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT GCT GCT GCT GCT (1.0000) 93 1 GTA (V) GTA (V) GTA (V) GTA (V) GTA (V) GTG (V) GTG (V) : GTA GTA GTA GTA GTG (0.9911) 94 1 GCT (A) GCT (A) GCT (A) GCT (A) ACT (T) GCC (A) GCC (A) : GCT GCT GCT GCT GCC (0.9373) 95 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) 96 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) 97 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG AAG AAG AAG AAG (0.9999) 98 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG AGG AGG AGG AGG (1.0000) 99 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT GTT GTT GTT GTT (0.9999) 100 1 GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC GTC GTC GTC GTC (1.0000) 101 1 CGT (R) CGC (R) AGT (S) AGT (S) AGT (S) CGT (R) CGC (R) : CGT CGT AGT AGT CGT (0.9153) 102 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) 103 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA CCA CCA CCA CCA (1.0000) 104 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA CAA CAA (1.0000) 105 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC GGC GGC GGC GGC (0.9999) 106 1 ATT (I) ATT (I) ATT (I) GTT (V) ATT (I) ATT (I) ATT (I) : ATT ATT ATT ATT ATT (0.9779) 107 1 AGA (R) AGA (R) CGA (R) CGA (R) AGA (R) AGA (R) AGG (R) : AGA AGA AGA CGA AGA (0.9144) 108 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) 109 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) 110 1 GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) : GTG GTG GTG GTG GTG (1.0000) 111 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) 112 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) 113 1 AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AAA (K) AAA (K) : AGA AGA AGA AGA AAA (0.9527) 114 1 AAT (N) AAT (N) AAG (K) AAT (N) AAT (N) GCT (A) GCT (A) : AAT AAT AAT AAT GCT (0.9702) 115 1 CGT (R) CGT (R) CAC (H) CAC (H) CAC (H) CAT (H) CAT (H) : CAT CGT CAC CAC CAT (0.9482) 116 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) 117 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA CAA CAA (1.0000) 118 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) 119 1 AGA (R) AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AGA (R) : AGA AGA AGA AGA AGA (0.9748) 120 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) 121 1 GTC (V) CTC (L) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC GTC GTC GTC GTC (0.9981) 122 1 CGT (R) CGT (R) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT CGT AGT AGT AGT (0.9920) 123 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG CAG CAG CAG CAG (1.0000) 124 1 TAT (Y) TAT (Y) TAT (Y) TAC (Y) TAT (Y) TAT (Y) TAT (Y) : TAT TAT TAT TAT TAT (0.9932) 125 1 GTT (V) ATT (I) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT GTT GTT GTT GTT (0.9882) 126 1 CAA (Q) CAA (Q) GAA (E) AAA (K) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA GAA CAA (0.5165) 127 1 GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) : GGT GGT GGT GGT GGT (0.9998) 128 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) 129 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) 130 1 GTG (V) GTA (V) GTA (V) GTG (V) GTG (V) GTA (V) GTA (V) : GTG GTG GTG GTG GTA (0.7827) List of extant and reconstructed sequences Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAC AAC ACA CGA GCT ACA AAC TAC AAT GCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AGT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG Hla_gibbon AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCC GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT CTC CGT CAG TAT ATT CAA GGT TGT GGA GTA Cgu/Can_colobus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAC GCT ACA AAC TAC AAT CCT GGA GAT GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AAA AAG CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTA Pne_langur AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT GAT GCC TGT CAT ATA TCC TGC AGT GCT TTG CTG CAA AAC AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC GTT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AAA GAT GTC AGT CAG TAC GTT AAA GGT TGT GGA GTG Mmu_rhesus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT AAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA ACT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG Ssc_squirrelM AAG GTC TTC GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG CTT GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAC TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT CAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA Cja_marmoset AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAC AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGG GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA node #8 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG node #9 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG node #10 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG node #11 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTG node #12 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA TREE # 2 Ancestral reconstruction by CODONML. ((Hsa_Human: 0.007565, Hla_gibbon: 0.011517): 0.020710, ((Cgu/Can_colobus: 0.012982, Pne_langur: 0.015429): 0.032838, Mmu_rhesus: 0.005766): 0.012982, (Ssc_squirrelM: 0.012140, Cja_marmoset: 0.007035): 0.035889); ((1, 2), ((3, 4), 5), (6, 7)); 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7 tree with node labels for Rod Page's TreeView ((1_Hsa_Human: 0.007565, 2_Hla_gibbon: 0.011517) 9 : 0.020710, ((3_Cgu/Can_colobus: 0.012982, 4_Pne_langur: 0.015429) 11 : 0.032838, 5_Mmu_rhesus: 0.005766) 10 : 0.012982, (6_Ssc_squirrelM: 0.012140, 7_Cja_marmoset: 0.007035) 12 : 0.035889) 8 ; Nodes 8 to 12 are ancestral (1) Marginal reconstruction of ancestral sequences (eqn. 4 in Yang et al. 1995 Genetics 141:1641-1650). Prob of best character at each node, listed by site Site Freq Data: 1 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) 2 1 GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) GTC (V) GTC (V) : GTC V 0.967 (V 0.967) GTC V 1.000 (V 1.000) ATC I 0.992 (I 0.992) ATC I 1.000 (I 1.000) GTC V 1.000 (V 1.000) 3 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTC (F) TTT (F) : TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 0.985 (F 1.000) 4 1 GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) : GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) 5 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) 6 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) 7 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) 8 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) 9 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) 10 1 AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) : AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) 11 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) 12 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) 13 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) 14 1 AGA (R) AGA (R) AAA (K) AAA (K) AGA (R) AGG (R) AGG (R) : AGA R 0.990 (R 1.000) AGA R 1.000 (R 1.000) AGA R 0.998 (R 0.998) AAA K 0.994 (K 0.994) AGG R 0.998 (R 1.000) 15 1 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) CTT (L) TTT (F) : TTG L 0.999 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTT F 0.990 (F 0.990) 16 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) 17 1 ATG (M) ATG (M) CTG (L) CTG (L) CTG (L) ATG (M) CTG (L) : CTG L 0.871 (L 0.871) ATG M 1.000 (M 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 0.871 (L 0.871) 18 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) 19 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) 20 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) 21 1 AGG (R) AGG (R) AAG (K) AAG (K) AGG (R) AGG (R) AGG (R) : AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 0.998 (R 0.998) AAG K 0.995 (K 0.995) AGG R 1.000 (R 1.000) 22 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) 23 1 ATC (I) ATC (I) GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) : ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 0.999 (I 0.999) GTC V 0.996 (V 0.996) ATC I 1.000 (I 1.000) 24 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) 25 1 CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) : CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) 26 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) 27 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) 28 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) 29 1 ATG (M) ATG (M) GTG (V) GTG (V) GTG (V) ATG (M) ATG (M) : ATG M 0.974 (M 0.974) ATG M 1.000 (M 1.000) GTG V 0.993 (V 0.993) GTG V 1.000 (V 1.000) ATG M 1.000 (M 1.000) 30 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) 31 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) 32 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) 33 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) 34 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) 35 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) 36 1 AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) 37 1 GGT (G) GGT (G) GGT (G) GGT (G) AAT (N) GAC (D) GAT (D) : GAT D 0.742 (D 0.743) GGT G 0.996 (G 0.996) GAT D 0.696 (D 0.696) GGT G 0.993 (G 0.993) GAT D 0.959 (D 0.999) 38 1 TAC (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT Y 0.999 (Y 1.000) TAT Y 0.962 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) 39 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) 40 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) 41 1 CGA (R) CGA (R) GAC (D) GAA (E) CAA (Q) CGT (R) CGT (R) : CGA R 0.977 (R 0.978) CGA R 1.000 (R 1.000) CAA Q 0.990 (Q 0.990) GAA E 0.992 (E 0.992) CGT R 1.000 (R 1.000) 42 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) 43 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) 44 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) 45 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) 46 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) 47 1 GCT (A) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) : CCT P 1.000 (P 1.000) CCT P 0.998 (P 0.998) CCT P 1.000 (P 1.000) CCT P 1.000 (P 1.000) CCT P 1.000 (P 1.000) 48 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) 49 1 GAC (D) GAC (D) GAT (D) GAC (D) GAC (D) GAC (D) GAC (D) : GAC D 1.000 (D 1.000) GAC D 1.000 (D 1.000) GAC D 1.000 (D 1.000) GAC D 0.989 (D 1.000) GAC D 1.000 (D 1.000) 50 1 AGA (R) AGA (R) GAA (E) GAA (E) CAA (Q) CAA (Q) CAA (Q) : CAA Q 0.980 (Q 0.980) AGA R 0.994 (R 0.995) CAA Q 0.990 (Q 0.990) GAA E 0.998 (E 0.998) CAA Q 1.000 (Q 1.000) 51 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) 52 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) 53 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) 54 1 TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) 55 1 GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) : GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) 56 1 ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) 57 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) : TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) 58 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) 59 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) 60 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) 61 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) 62 1 CGC (R) CGC (R) CGC (R) CGC (R) CAC (H) CAC (H) CAC (H) : CAC H 0.742 (H 0.742) CGC R 0.999 (R 0.999) CAC H 0.748 (H 0.748) CGC R 0.998 (R 0.998) CAC H 1.000 (H 1.000) 63 1 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAT (Y) TAT (Y) : TAC Y 0.994 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAT Y 0.997 (Y 1.000) 64 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) 65 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) 66 1 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAC (N) : AAT N 0.998 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 0.889 (N 1.000) 67 1 GAT (D) GAT (D) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT N 0.970 (N 0.970) GAT D 0.994 (D 0.994) AAT N 0.999 (N 0.999) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) 68 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) 69 1 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AGA (R) AGA (R) : AAA K 0.992 (K 0.992) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AGA R 0.998 (R 0.998) 70 1 ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) : ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) 71 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) 72 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) 73 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) 74 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) 75 1 AAT (N) AAT (N) AAT (N) GAT (D) AAT (N) AAT (N) AAT (N) : AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 0.964 (N 0.964) AAT N 1.000 (N 1.000) 76 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) 77 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) 78 1 CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) : CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) 79 1 TTA (L) TTA (L) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA I 0.997 (I 0.997) TTA L 1.000 (L 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) 80 1 TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) : TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) 81 1 TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) : TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) 82 1 AGT (S) AAT (N) AAT (N) AGT (S) AAT (N) AAT (N) AAT (N) : AAT N 0.998 (N 0.998) AAT N 0.957 (N 0.957) AAT N 0.999 (N 0.999) AAT N 0.963 (N 0.963) AAT N 1.000 (N 1.000) 83 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) 84 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) 85 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) 86 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) 87 1 GAT (D) GAT (D) AAT (N) AAC (N) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 0.996 (D 0.997) AAT N 0.983 (N 0.993) GAT D 1.000 (D 1.000) 88 1 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) GAC (D) GAC (D) : AAC N 0.993 (N 0.993) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) GAC D 0.998 (D 0.998) 89 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) 90 1 GCT (A) GCC (A) GCT (A) GCT (A) GCT (A) ACT (T) ACT (T) : GCT A 0.994 (A 0.994) GCT A 0.985 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) ACT T 0.998 (T 0.998) 91 1 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) CAA (Q) GAA (E) : GAT D 0.997 (D 0.997) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAA E 0.995 (E 0.995) 92 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) 93 1 GTA (V) GTA (V) GTA (V) GTA (V) GTA (V) GTG (V) GTG (V) : GTA V 0.993 (V 1.000) GTA V 1.000 (V 1.000) GTA V 1.000 (V 1.000) GTA V 1.000 (V 1.000) GTG V 0.998 (V 1.000) 94 1 GCT (A) GCT (A) GCT (A) GCT (A) ACT (T) GCC (A) GCC (A) : GCT A 0.990 (A 0.998) GCT A 1.000 (A 1.000) GCT A 0.947 (A 0.947) GCT A 1.000 (A 1.000) GCC A 0.998 (A 1.000) 95 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) 96 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) 97 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) 98 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) 99 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) 100 1 GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) 101 1 CGT (R) CGC (R) AGT (S) AGT (S) AGT (S) CGT (R) CGC (R) : CGT R 0.973 (R 0.993) CGT R 0.970 (R 1.000) AGT S 0.995 (S 0.996) AGT S 1.000 (S 1.000) CGT R 0.935 (R 1.000) 102 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) 103 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) 104 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) 105 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) 106 1 ATT (I) ATT (I) ATT (I) GTT (V) ATT (I) ATT (I) ATT (I) : ATT I 1.000 (I 1.000) ATT I 1.000 (I 1.000) ATT I 1.000 (I 1.000) ATT I 0.978 (I 0.978) ATT I 1.000 (I 1.000) 107 1 AGA (R) AGA (R) CGA (R) CGA (R) AGA (R) AGA (R) AGG (R) : AGA R 0.999 (R 1.000) AGA R 1.000 (R 1.000) AGA R 0.996 (R 1.000) CGA R 0.996 (R 1.000) AGA R 0.921 (R 1.000) 108 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) 109 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) 110 1 GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) : GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) 111 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) 112 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) 113 1 AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AAA (K) AAA (K) : AGA R 0.990 (R 0.990) AGA R 1.000 (R 1.000) AGA R 0.997 (R 0.997) AGA R 0.962 (R 0.962) AAA K 0.998 (K 0.998) 114 1 AAT (N) AAT (N) AAG (K) AAT (N) AAT (N) GCT (A) GCT (A) : AAT N 0.984 (N 0.984) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 0.987 (N 0.988) GCT A 0.998 (A 0.998) 115 1 CGT (R) CGT (R) CAC (H) CAC (H) CAC (H) CAT (H) CAT (H) : CAT H 0.952 (H 0.990) CGT R 0.998 (R 0.998) CAC H 0.998 (H 1.000) CAC H 1.000 (H 1.000) CAT H 1.000 (H 1.000) 116 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) 117 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) 118 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) 119 1 AGA (R) AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AGA (R) : AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 0.975 (R 0.975) AGA R 1.000 (R 1.000) 120 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) 121 1 GTC (V) CTC (L) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC V 1.000 (V 1.000) GTC V 0.998 (V 0.998) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) 122 1 CGT (R) CGT (R) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT S 0.993 (S 0.993) CGT R 0.999 (R 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) 123 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) 124 1 TAT (Y) TAT (Y) TAT (Y) TAC (Y) TAT (Y) TAT (Y) TAT (Y) : TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 0.993 (Y 1.000) TAT Y 1.000 (Y 1.000) 125 1 GTT (V) ATT (I) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT V 1.000 (V 1.000) GTT V 0.988 (V 0.988) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) 126 1 CAA (Q) CAA (Q) GAA (E) AAA (K) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) GAA E 0.517 (E 0.517) CAA Q 1.000 (Q 1.000) 127 1 GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) : GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) 128 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) 129 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) 130 1 GTG (V) GTA (V) GTA (V) GTG (V) GTG (V) GTA (V) GTA (V) : GTG V 0.797 (V 1.000) GTG V 0.795 (V 1.000) GTG V 0.942 (V 1.000) GTG V 0.937 (V 1.000) GTA V 0.998 (V 1.000) Summary of changes along branches. Check root for directions of change. Branch 1: 8..9 (n= 8.5 s= 0.5) 17 L 0.871 -> M 1.000 37 D 0.743 -> G 0.996 50 Q 0.980 -> R 0.995 62 H 0.742 -> R 0.999 67 N 0.970 -> D 0.994 79 I 0.997 -> L 1.000 115 H 0.990 -> R 0.998 122 S 0.993 -> R 1.000 Branch 2: 9..1 (Hsa_Human) (n= 2.0 s= 1.0) 47 P 0.998 -> A 82 N 0.957 -> S Branch 3: 9..2 (Hla_gibbon) (n= 2.0 s= 3.0) 121 V 0.998 -> L 125 V 0.988 -> I Branch 4: 8..10 (n= 4.0 s= 1.0) 2 V 0.967 -> I 0.992 29 M 0.974 -> V 0.993 41 R 0.978 -> Q 0.990 101 R 0.993 -> S 0.996 Branch 5: 10..11 (n= 9.0 s= 1.0) 14 R 0.998 -> K 0.994 21 R 0.998 -> K 0.995 23 I 0.999 -> V 0.996 37 D 0.696 -> G 0.993 41 Q 0.990 -> E 0.992 50 Q 0.990 -> E 0.998 62 H 0.748 -> R 0.998 87 D 0.997 -> N 0.993 126 Q 1.000 -> E 0.517 Branch 6: 11..3 (Cgu/Can_colobus) (n= 3.0 s= 2.0) 41 E 0.992 -> D 113 R 0.962 -> K 114 N 0.988 -> K Branch 7: 11..4 (Pne_langur) (n= 5.0 s= 2.0) 75 N 0.964 -> D 82 N 0.963 -> S 106 I 0.978 -> V 119 R 0.975 -> K 126 E 0.517 -> K Branch 8: 10..5 (Mmu_rhesus) (n= 2.0 s= 0.0) 37 D 0.696 -> N 94 A 0.947 -> T Branch 9: 8..12 (n= 8.0 s= 6.0) 15 L 1.000 -> F 0.990 69 K 0.992 -> R 0.998 88 N 0.993 -> D 0.998 90 A 0.994 -> T 0.998 91 D 0.997 -> E 0.995 113 R 0.990 -> K 0.998 114 N 0.984 -> A 0.998 Branch 10: 12..6 (Ssc_squirrelM) (n= 3.0 s= 2.0) 15 F 0.990 -> L 17 L 0.871 -> M 91 E 0.995 -> Q Branch 11: 12..7 (Cja_marmoset) (n= 0.0 s= 3.0) List of extant and reconstructed sequences Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAC AAC ACA CGA GCT ACA AAC TAC AAT GCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AGT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG Hla_gibbon AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCC GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT CTC CGT CAG TAT ATT CAA GGT TGT GGA GTA Cgu/Can_colobus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAC GCT ACA AAC TAC AAT CCT GGA GAT GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AAA AAG CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTA Pne_langur AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT GAT GCC TGT CAT ATA TCC TGC AGT GCT TTG CTG CAA AAC AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC GTT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AAA GAT GTC AGT CAG TAC GTT AAA GGT TGT GGA GTG Mmu_rhesus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT AAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA ACT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG Ssc_squirrelM AAG GTC TTC GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG CTT GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAC TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT CAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA Cja_marmoset AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAC AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGG GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA node #8 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG node #9 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG node #10 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG node #11 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTG node #12 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA Overall accuracy of the 5 ancestral sequences: 0.99108 0.99716 0.99439 0.99393 0.99633 for a site. 0.27875 0.67341 0.43633 0.37872 0.60699 for the sequence. Amino acid sequences inferred by codonml. Node #8 KVFERCELAR TLKRLGLDGY RGISLANWMC LAKWESDYNT RATNYNPGDQ STDYGIFQIN SHYWCNNGKT PGAVNACHIS CNALLQDNIA DAVACAKRVV RDPQGIRAWV AWRNHCQNRD VSQYVQGCGV Node #9 KVFERCELAR TLKRLGMDGY RGISLANWMC LAKWESGYNT RATNYNPGDR STDYGIFQIN SRYWCNDGKT PGAVNACHLS CNALLQDNIA DAVACAKRVV RDPQGIRAWV AWRNRCQNRD VRQYVQGCGV Node #10 KIFERCELAR TLKRLGLDGY RGISLANWVC LAKWESDYNT QATNYNPGDQ STDYGIFQIN SHYWCNNGKT PGAVNACHIS CNALLQDNIA DAVACAKRVV SDPQGIRAWV AWRNHCQNRD VSQYVQGCGV Node #11 KIFERCELAR TLKKLGLDGY KGVSLANWVC LAKWESGYNT EATNYNPGDE STDYGIFQIN SRYWCNNGKT PGAVNACHIS CNALLQNNIA DAVACAKRVV SDPQGIRAWV AWRNHCQNRD VSQYVEGCGV Node #12 KVFERCELAR TLKRFGLDGY RGISLANWMC LAKWESDYNT RATNYNPGDQ STDYGIFQIN SHYWCNNGRT PGAVNACHIS CNALLQDDIT EAVACAKRVV RDPQGIRAWV AWKAHCQNRD VSQYVQGCGV Changes at sites (syn nonsyn). 1 (0.0 0.0) 2 GTC.ATC (0.0 1.0) 3 TTT.TTC (1.0 0.0) 4 (0.0 0.0) 5 (0.0 0.0) 6 (0.0 0.0) 7 (0.0 0.0) 8 (0.0 0.0) 9 (0.0 0.0) 10 (0.0 0.0) 11 (0.0 0.0) 12 (0.0 0.0) 13 (0.0 0.0) 14 AGA.AAA AGA.AGG (1.0 1.0) 15 TTT.CTT TTG.TTT (0.0 2.0) 16 (0.0 0.0) 17 CTG.ATG CTG.ATG (0.0 2.0) 18 (0.0 0.0) 19 (0.0 0.0) 20 (0.0 0.0) 21 AGG.AAG (0.0 1.0) 22 (0.0 0.0) 23 ATC.GTC (0.0 1.0) 24 (0.0 0.0) 25 (0.0 0.0) 26 (0.0 0.0) 27 (0.0 0.0) 28 (0.0 0.0) 29 ATG.GTG (0.0 1.0) 30 (0.0 0.0) 31 (0.0 0.0) 32 (0.0 0.0) 33 (0.0 0.0) 34 (0.0 0.0) 35 (0.0 0.0) 36 (0.0 0.0) 37 GAT.AAT GAT.GAC GAT.GGT GAT.GGT (1.0 3.0) 38 TAT.TAC (1.0 0.0) 39 (0.0 0.0) 40 (0.0 0.0) 41 GAA.GAC CGA.CAA CAA.GAA CGA.CGT (1.0 3.0) 42 (0.0 0.0) 43 (0.0 0.0) 44 (0.0 0.0) 45 (0.0 0.0) 46 (0.0 0.0) 47 CCT.GCT (0.0 1.0) 48 (0.0 0.0) 49 GAC.GAT (1.0 0.0) 50 CAA.AGA CAA.GAA (0.5 2.5) 51 (0.0 0.0) 52 (0.0 0.0) 53 (0.0 0.0) 54 (0.0 0.0) 55 (0.0 0.0) 56 (0.0 0.0) 57 (0.0 0.0) 58 (0.0 0.0) 59 (0.0 0.0) 60 (0.0 0.0) 61 (0.0 0.0) 62 CAC.CGC CAC.CGC (0.0 2.0) 63 TAC.TAT (1.0 0.0) 64 (0.0 0.0) 65 (0.0 0.0) 66 AAT.AAC (1.0 0.0) 67 AAT.GAT (0.0 1.0) 68 (0.0 0.0) 69 AAA.AGA (0.0 1.0) 70 (0.0 0.0) 71 (0.0 0.0) 72 (0.0 0.0) 73 (0.0 0.0) 74 (0.0 0.0) 75 AAT.GAT (0.0 1.0) 76 (0.0 0.0) 77 (0.0 0.0) 78 (0.0 0.0) 79 ATA.TTA (0.0 1.0) 80 (0.0 0.0) 81 (0.0 0.0) 82 AAT.AGT AAT.AGT (0.0 2.0) 83 (0.0 0.0) 84 (0.0 0.0) 85 (0.0 0.0) 86 (0.0 0.0) 87 AAT.AAC GAT.AAT (1.0 1.0) 88 AAC.GAC (0.0 1.0) 89 (0.0 0.0) 90 GCT.GCC GCT.ACT (1.0 1.0) 91 GAA.CAA GAT.GAA (0.0 2.0) 92 (0.0 0.0) 93 GTA.GTG (1.0 0.0) 94 GCT.ACT GCT.GCC (1.0 1.0) 95 (0.0 0.0) 96 (0.0 0.0) 97 (0.0 0.0) 98 (0.0 0.0) 99 (0.0 0.0) 100 (0.0 0.0) 101 CGT.CGC CGT.CGC CGT.AGT (2.0 1.0) 102 (0.0 0.0) 103 (0.0 0.0) 104 (0.0 0.0) 105 (0.0 0.0) 106 ATT.GTT (0.0 1.0) 107 AGA.AGG AGA.CGA (2.0 0.0) 108 (0.0 0.0) 109 (0.0 0.0) 110 (0.0 0.0) 111 (0.0 0.0) 112 (0.0 0.0) 113 AGA.AAA AGA.AAA (0.0 2.0) 114 AAT.AAG AAT.GCT (0.0 3.0) 115 CAT.CGT CAT.CAC (1.0 1.0) 116 (0.0 0.0) 117 (0.0 0.0) 118 (0.0 0.0) 119 AGA.AAA (0.0 1.0) 120 (0.0 0.0) 121 GTC.CTC (0.0 1.0) 122 AGT.CGT (0.0 1.0) 123 (0.0 0.0) 124 TAT.TAC (1.0 0.0) 125 GTT.ATT (0.0 1.0) 126 GAA.AAA CAA.GAA (0.0 2.0) 127 (0.0 0.0) 128 (0.0 0.0) 129 (0.0 0.0) 130 GTG.GTA GTG.GTA GTG.GTA (3.0 0.0) (2) Joint reconstruction of ancestral sequences (eqn. 2 in Yang et al. 1995 Genetics 141:1641-1650), using the algorithm of Pupko et al. (2000 Mol Biol Evol 17:890-896). Listed by site, reconstruction (prob.) Site Freq Data: 1 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG AAG AAG AAG AAG (0.9999) 2 1 GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) GTC (V) GTC (V) : GTC GTC ATC ATC GTC (0.9589) 3 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTC (F) TTT (F) : TTT TTT TTT TTT TTT (0.9846) 4 1 GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) : GAA GAA GAA GAA GAA (0.9999) 5 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG AGG AGG AGG AGG (1.0000) 6 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) 7 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG GAG GAG GAG GAG (0.9999) 8 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG TTG TTG TTG TTG (1.0000) 9 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC GCC GCC GCC GCC (1.0000) 10 1 AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) : AGA AGA AGA AGA AGA (0.9999) 11 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT ACT ACT ACT ACT (1.0000) 12 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG CTG CTG CTG CTG (1.0000) 13 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA AAA AAA AAA AAA (0.9999) 14 1 AGA (R) AGA (R) AAA (K) AAA (K) AGA (R) AGG (R) AGG (R) : AGA AGA AGA AAA AGG (0.9789) 15 1 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) CTT (L) TTT (F) : TTG TTG TTG TTG TTT (0.9894) 16 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) 17 1 ATG (M) ATG (M) CTG (L) CTG (L) CTG (L) ATG (M) CTG (L) : CTG ATG CTG CTG CTG (0.8701) 18 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) 19 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC GGC GGC GGC GGC (0.9999) 20 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC TAC TAC TAC TAC (1.0000) 21 1 AGG (R) AGG (R) AAG (K) AAG (K) AGG (R) AGG (R) AGG (R) : AGG AGG AGG AAG AGG (0.9935) 22 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) 23 1 ATC (I) ATC (I) GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) : ATC ATC ATC GTC ATC (0.9950) 24 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC AGC AGC AGC AGC (0.9999) 25 1 CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) : CTA CTA CTA CTA CTA (1.0000) 26 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) 27 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) 28 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) 29 1 ATG (M) ATG (M) GTG (V) GTG (V) GTG (V) ATG (M) ATG (M) : ATG ATG GTG GTG ATG (0.9668) 30 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) 31 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG TTG TTG TTG TTG (1.0000) 32 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC GCC GCC GCC GCC (1.0000) 33 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA AAA AAA AAA AAA (0.9999) 34 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) 35 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG GAG GAG GAG GAG (0.9999) 36 1 AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT AGT AGT AGT AGT (0.9998) 37 1 GGT (G) GGT (G) GGT (G) GGT (G) AAT (N) GAC (D) GAT (D) : GAT GGT GAT GGT GAT (0.6376) 38 1 TAC (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT TAT TAT TAT TAT (0.9616) 39 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) 40 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA ACA ACA ACA ACA (1.0000) 41 1 CGA (R) CGA (R) GAC (D) GAA (E) CAA (Q) CGT (R) CGT (R) : CGA CGA CAA GAA CGT (0.9586) 42 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT GCT GCT GCT GCT (1.0000) 43 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA ACA ACA ACA ACA (1.0000) 44 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) 45 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC TAC TAC TAC TAC (1.0000) 46 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9998) 47 1 GCT (A) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) : CCT CCT CCT CCT CCT (0.9979) 48 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) 49 1 GAC (D) GAC (D) GAT (D) GAC (D) GAC (D) GAC (D) GAC (D) : GAC GAC GAC GAC GAC (0.9890) 50 1 AGA (R) AGA (R) GAA (E) GAA (E) CAA (Q) CAA (Q) CAA (Q) : CAA AGA CAA GAA CAA (0.9726) 51 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC AGC AGC AGC AGC (0.9999) 52 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT ACT ACT ACT ACT (1.0000) 53 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) 54 1 TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT TAT TAT TAT TAT (1.0000) 55 1 GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) : GGG GGG GGG GGG GGG (1.0000) 56 1 ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA ATA ATA ATA ATA (1.0000) 57 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) : TTT TTT TTT TTT TTT (1.0000) 58 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG CAG CAG CAG CAG (1.0000) 59 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC ATC ATC ATC ATC (1.0000) 60 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9998) 61 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC AGC AGC AGC AGC (0.9999) 62 1 CGC (R) CGC (R) CGC (R) CGC (R) CAC (H) CAC (H) CAC (H) : CAC CGC CAC CGC CAC (0.7383) 63 1 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAT (Y) TAT (Y) : TAC TAC TAC TAC TAT (0.9908) 64 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) 65 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) 66 1 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAC (N) : AAT AAT AAT AAT AAT (0.8888) 67 1 GAT (D) GAT (D) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT GAT AAT AAT AAT (0.9642) 68 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC GGC GGC GGC GGC (0.9999) 69 1 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AGA (R) AGA (R) : AAA AAA AAA AAA AGA (0.9899) 70 1 ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) : ACC ACC ACC ACC ACC (1.0000) 71 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA CCA CCA CCA CCA (1.0000) 72 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) 73 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) 74 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT GTT GTT GTT GTT (0.9999) 75 1 AAT (N) AAT (N) AAT (N) GAT (D) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9638) 76 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC GCC GCC GCC GCC (1.0000) 77 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) 78 1 CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) : CAT CAT CAT CAT CAT (1.0000) 79 1 TTA (L) TTA (L) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA TTA ATA ATA ATA (0.9961) 80 1 TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) : TCC TCC TCC TCC TCC (1.0000) 81 1 TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) : TGC TGC TGC TGC TGC (1.0000) 82 1 AGT (S) AAT (N) AAT (N) AGT (S) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9224) 83 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT GCT GCT GCT GCT (1.0000) 84 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG TTG TTG TTG TTG (1.0000) 85 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG CTG CTG CTG CTG (1.0000) 86 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA CAA CAA (1.0000) 87 1 GAT (D) GAT (D) AAT (N) AAC (N) GAT (D) GAT (D) GAT (D) : GAT GAT GAT AAT GAT (0.9799) 88 1 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) GAC (D) GAC (D) : AAC AAC AAC AAC GAC (0.9905) 89 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC ATC ATC ATC ATC (1.0000) 90 1 GCT (A) GCC (A) GCT (A) GCT (A) GCT (A) ACT (T) ACT (T) : GCT GCT GCT GCT ACT (0.9782) 91 1 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) CAA (Q) GAA (E) : GAT GAT GAT GAT GAA (0.9916) 92 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT GCT GCT GCT GCT (1.0000) 93 1 GTA (V) GTA (V) GTA (V) GTA (V) GTA (V) GTG (V) GTG (V) : GTA GTA GTA GTA GTG (0.9911) 94 1 GCT (A) GCT (A) GCT (A) GCT (A) ACT (T) GCC (A) GCC (A) : GCT GCT GCT GCT GCC (0.9373) 95 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) 96 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) 97 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG AAG AAG AAG AAG (0.9999) 98 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG AGG AGG AGG AGG (1.0000) 99 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT GTT GTT GTT GTT (0.9999) 100 1 GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC GTC GTC GTC GTC (1.0000) 101 1 CGT (R) CGC (R) AGT (S) AGT (S) AGT (S) CGT (R) CGC (R) : CGT CGT AGT AGT CGT (0.9153) 102 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) 103 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA CCA CCA CCA CCA (1.0000) 104 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA CAA CAA (1.0000) 105 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC GGC GGC GGC GGC (0.9999) 106 1 ATT (I) ATT (I) ATT (I) GTT (V) ATT (I) ATT (I) ATT (I) : ATT ATT ATT ATT ATT (0.9779) 107 1 AGA (R) AGA (R) CGA (R) CGA (R) AGA (R) AGA (R) AGG (R) : AGA AGA AGA CGA AGA (0.9144) 108 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) 109 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) 110 1 GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) : GTG GTG GTG GTG GTG (1.0000) 111 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) 112 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) 113 1 AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AAA (K) AAA (K) : AGA AGA AGA AGA AAA (0.9527) 114 1 AAT (N) AAT (N) AAG (K) AAT (N) AAT (N) GCT (A) GCT (A) : AAT AAT AAT AAT GCT (0.9702) 115 1 CGT (R) CGT (R) CAC (H) CAC (H) CAC (H) CAT (H) CAT (H) : CAT CGT CAC CAC CAT (0.9482) 116 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) 117 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA CAA CAA (1.0000) 118 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) 119 1 AGA (R) AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AGA (R) : AGA AGA AGA AGA AGA (0.9748) 120 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) 121 1 GTC (V) CTC (L) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC GTC GTC GTC GTC (0.9981) 122 1 CGT (R) CGT (R) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT CGT AGT AGT AGT (0.9920) 123 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG CAG CAG CAG CAG (1.0000) 124 1 TAT (Y) TAT (Y) TAT (Y) TAC (Y) TAT (Y) TAT (Y) TAT (Y) : TAT TAT TAT TAT TAT (0.9932) 125 1 GTT (V) ATT (I) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT GTT GTT GTT GTT (0.9882) 126 1 CAA (Q) CAA (Q) GAA (E) AAA (K) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA GAA CAA (0.5165) 127 1 GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) : GGT GGT GGT GGT GGT (0.9998) 128 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) 129 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) 130 1 GTG (V) GTA (V) GTA (V) GTG (V) GTG (V) GTA (V) GTA (V) : GTG GTG GTG GTG GTA (0.7827) List of extant and reconstructed sequences Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAC AAC ACA CGA GCT ACA AAC TAC AAT GCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AGT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG Hla_gibbon AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCC GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT CTC CGT CAG TAT ATT CAA GGT TGT GGA GTA Cgu/Can_colobus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAC GCT ACA AAC TAC AAT CCT GGA GAT GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AAA AAG CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTA Pne_langur AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT GAT GCC TGT CAT ATA TCC TGC AGT GCT TTG CTG CAA AAC AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC GTT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AAA GAT GTC AGT CAG TAC GTT AAA GGT TGT GGA GTG Mmu_rhesus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT AAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA ACT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG Ssc_squirrelM AAG GTC TTC GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG CTT GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAC TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT CAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA Cja_marmoset AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAC AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGG GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA node #8 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG node #9 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG node #10 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG node #11 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTG node #12 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml_lysozyme/2NG.dN0000644000175000017500000000051113316145226023414 0ustar carandraugcarandraug 7 Hsa_Human Hla_gibbon 0.0133 Cgu/Can_colobus 0.0742 0.0742 Pne_langur 0.0725 0.0797 0.0267 Mmu_rhesus 0.0562 0.0561 0.0473 0.0508 Ssc_squirrelM 0.0633 0.0633 0.0775 0.0959 0.0559 Cja_marmoset 0.0634 0.0633 0.0704 0.0886 0.0490 0.0099 Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml_lysozyme/rub0000644000175000017500000001557613316145226023277 0ustar carandraugcarandraug TREE # 1 1 57.0511 911.866966 x: 0.06268 0.02434 0.03918 0.04580 0.06920 0.04580 0.05520 0.02250 0.11892 0.03972 0.02397 2.00271 0.99739 1.00045 2 18.9464 911.763959 x: 0.06764 0.02691 0.03838 0.04277 0.07495 0.04374 0.05085 0.02078 0.12004 0.03946 0.02493 2.00731 0.99290 1.00125 3 17.2055 911.691402 x: 0.06952 0.02343 0.03790 0.04130 0.07813 0.04241 0.05090 0.02232 0.12022 0.03952 0.02308 2.01485 0.98551 1.00259 4 41.0047 910.628609 x: 0.07137 0.02620 0.04439 0.03804 0.09645 0.03989 0.07654 0.01714 0.11898 0.04587 0.02567 2.18502 0.81862 1.03300 5 330.0384 908.660991 x: 0.07033 0.03282 0.03599 0.04791 0.09682 0.04206 0.07188 0.02569 0.11667 0.03794 0.02291 2.45879 0.55009 1.08221 6 273.9810 908.174440 x: 0.06841 0.02641 0.03736 0.04422 0.09012 0.04075 0.06501 0.01808 0.11687 0.04088 0.02517 2.53001 0.48216 1.09516 7 32.0852 908.121354 x: 0.06962 0.02714 0.04113 0.04201 0.08801 0.04202 0.06373 0.01990 0.11788 0.04271 0.02403 2.53971 0.47611 1.09709 8 10.2883 908.049989 x: 0.07394 0.02754 0.03882 0.04039 0.08345 0.04272 0.06595 0.01893 0.12390 0.04249 0.02214 2.56256 0.47895 1.10243 9 43.9147 907.929599 x: 0.07633 0.02582 0.03897 0.04193 0.08067 0.04109 0.06609 0.02170 0.13092 0.04309 0.02766 2.60763 0.48889 1.11319 10 113.4636 907.253062 x: 0.06522 0.02536 0.04672 0.04661 0.08046 0.03475 0.05796 0.01902 0.14707 0.03974 0.02253 2.85340 0.55093 1.17235 11 321.0222 906.555179 x: 0.05575 0.02365 0.04095 0.03870 0.08148 0.04813 0.04995 0.01976 0.14572 0.04344 0.02458 3.11682 0.61923 1.23610 12 218.4010 905.867140 x: 0.06763 0.02337 0.04059 0.04004 0.07126 0.04482 0.04620 0.01794 0.11796 0.04643 0.02419 3.36606 0.68506 1.29708 13 10.3815 905.858148 x: 0.06797 0.02299 0.04143 0.03927 0.07104 0.04529 0.04644 0.01777 0.11741 0.04411 0.02477 3.36949 0.68592 1.29825 14 0.9990 904.942858 x: 0.07115 0.02876 0.03573 0.04652 0.08159 0.04513 0.05585 0.02212 0.11829 0.03704 0.02354 3.94359 0.69088 2.38587 15 0.3806 904.698026 x: 0.07011 0.02501 0.04000 0.04494 0.07830 0.04277 0.05139 0.01930 0.12412 0.04343 0.02357 4.29118 0.68983 2.81855 16 0.2244 904.645420 x: 0.06969 0.02541 0.03882 0.04333 0.07840 0.04396 0.05141 0.01939 0.12040 0.04029 0.02387 4.54266 0.68846 3.09347 17 0.0853 904.640565 x: 0.06999 0.02558 0.03888 0.04375 0.07907 0.04392 0.05259 0.01951 0.12142 0.04125 0.02378 4.58691 0.68596 3.19513 18 0.0476 904.639140 x: 0.07001 0.02561 0.03907 0.04408 0.07910 0.04381 0.05186 0.01956 0.12174 0.04098 0.02376 4.60048 0.68393 3.28862 19 0.0549 904.636957 x: 0.07016 0.02550 0.03890 0.04390 0.07906 0.04381 0.05212 0.01934 0.12067 0.04109 0.02378 4.57807 0.68577 3.47164 20 0.0294 904.636560 x: 0.07006 0.02557 0.03891 0.04387 0.07901 0.04390 0.05216 0.01948 0.12134 0.04102 0.02378 4.56178 0.68562 3.50174 21 0.0035 904.636554 x: 0.07001 0.02557 0.03893 0.04388 0.07905 0.04388 0.05215 0.01949 0.12130 0.04104 0.02378 4.56086 0.68574 3.50529 22 0.0004 904.636553 x: 0.07000 0.02557 0.03893 0.04388 0.07904 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56116 0.68580 3.50580 23 0.0001 904.636553 x: 0.07000 0.02557 0.03893 0.04388 0.07904 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56117 0.68580 3.50577 24 0.0001 904.636553 x: 0.07000 0.02557 0.03893 0.04388 0.07904 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56118 0.68580 3.50575 25 0.0000 904.636553 x: 0.07000 0.02557 0.03893 0.04388 0.07904 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56118 0.68580 3.50575 TREE # 2 1 64.8459 904.711965 x: 0.06603 0.02485 0.04005 0.04745 0.07283 0.04652 0.05480 0.01985 0.11993 0.04141 0.02359 4.56116 0.68595 3.50574 2 17.6419 904.639797 x: 0.07001 0.02633 0.03883 0.04446 0.07825 0.04417 0.05145 0.01925 0.12104 0.04098 0.02420 4.56116 0.68598 3.50574 3 4.6734 904.636959 x: 0.07020 0.02548 0.03884 0.04411 0.07884 0.04400 0.05172 0.01950 0.12114 0.04097 0.02372 4.56116 0.68598 3.50574 4 1.3499 904.636631 x: 0.07016 0.02554 0.03899 0.04395 0.07907 0.04400 0.05210 0.01938 0.12122 0.04106 0.02378 4.56116 0.68597 3.50574 5 0.3002 904.636616 x: 0.07014 0.02557 0.03898 0.04399 0.07911 0.04400 0.05213 0.01944 0.12126 0.04106 0.02378 4.56116 0.68597 3.50574 6 0.1248 904.636613 x: 0.07012 0.02556 0.03896 0.04401 0.07913 0.04399 0.05213 0.01942 0.12130 0.04105 0.02378 4.56116 0.68597 3.50574 7 0.0510 904.636612 x: 0.07011 0.02556 0.03898 0.04400 0.07912 0.04399 0.05212 0.01943 0.12132 0.04106 0.02378 4.56116 0.68597 3.50574 8 0.0209 904.636612 x: 0.07011 0.02556 0.03897 0.04400 0.07912 0.04399 0.05212 0.01943 0.12133 0.04106 0.02378 4.56116 0.68596 3.50574 9 0.0161 904.636612 x: 0.07012 0.02556 0.03897 0.04400 0.07911 0.04399 0.05212 0.01943 0.12134 0.04106 0.02378 4.56116 0.68596 3.50574 10 0.0156 904.636611 x: 0.07012 0.02556 0.03898 0.04401 0.07911 0.04398 0.05212 0.01943 0.12134 0.04105 0.02378 4.56116 0.68592 3.50574 11 0.0916 904.636598 x: 0.07010 0.02556 0.03896 0.04398 0.07911 0.04397 0.05212 0.01943 0.12132 0.04105 0.02378 4.56121 0.68506 3.50574 12 0.0063 904.636596 x: 0.07009 0.02557 0.03896 0.04398 0.07911 0.04396 0.05212 0.01944 0.12132 0.04108 0.02377 4.56122 0.68508 3.50574 13 0.0706 904.636554 x: 0.07001 0.02557 0.03893 0.04387 0.07905 0.04388 0.05214 0.01948 0.12131 0.04103 0.02378 4.56129 0.68581 3.50574 14 0.0001 904.636553 x: 0.07000 0.02557 0.03893 0.04388 0.07905 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56124 0.68581 3.50574 15 0.0000 904.636553 x: 0.07000 0.02557 0.03893 0.04388 0.07905 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56122 0.68581 3.50574 16 0.0000 904.636553 x: 0.07000 0.02557 0.03893 0.04388 0.07905 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56122 0.68581 3.50574 Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml_lysozyme/lnf0000644000175000017500000004025313316145226023254 0ustar carandraugcarandraug 2 130 81 1 1 2 -4.4631936441 1.4983 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) 2 1 -9.5051356295 0.0097 GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) GTC (V) GTC (V) 3 1 -9.7022173688 0.0079 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTC (F) TTT (F) 4 1 -4.2039253720 1.9418 GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) 5 2 -4.5556175232 1.3660 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) 6 7 -4.3823910150 1.6244 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) 7 2 -4.4321334372 1.5456 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) 8 3 -5.0765672523 0.8114 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) 9 3 -4.7615724447 1.1118 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) 10 1 -4.3184529418 1.7317 AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) 11 2 -4.5084067380 1.4321 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) 12 2 -5.4399561134 0.5642 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) 13 2 -4.2372969984 1.8781 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) 14 1 -10.9655217803 0.0022 AGA (R) AGA (R) AAA (K) AAA (K) AGA (R) AGG (R) AGG (R) 15 1 -16.0576876241 0.0000 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) CTT (L) TTT (F) 16 5 -4.3016142564 1.7611 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) 17 1 -18.1074372042 0.0000 ATG (M) ATG (M) CTG (L) CTG (L) CTG (L) ATG (M) CTG (L) 18 4 -4.1086751238 2.1358 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) 19 3 -4.4725258929 1.4844 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) 20 2 -4.5810698348 1.3317 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) 21 1 -8.2006772519 0.0357 AGG (R) AGG (R) AAG (K) AAG (K) AGG (R) AGG (R) AGG (R) 22 1 -8.6032910323 0.0239 ATC (I) ATC (I) GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) 23 3 -4.4856422368 1.4651 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) 24 1 -5.2057180378 0.7131 CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) 25 5 -4.6403385123 1.2551 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) 26 4 -4.4201645295 1.5642 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) 27 5 -4.5973658698 1.3102 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) 28 1 -9.7392781217 0.0077 ATG (M) ATG (M) GTG (V) GTG (V) GTG (V) ATG (M) ATG (M) 29 1 -4.2139700025 1.9224 AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) 30 1 -19.3633273590 0.0000 GGT (G) GGT (G) GGT (G) GGT (G) AAT (N) GAC (D) GAT (D) 31 1 -9.2797480927 0.0121 TAC (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) 32 2 -4.6757503564 1.2114 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) 33 1 -25.8812469730 0.0000 CGA (R) CGA (R) GAC (D) GAA (E) CAA (Q) CGT (R) CGT (R) 34 3 -4.4744717992 1.4815 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) 35 2 -4.1412516220 2.0674 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) 36 1 -11.8290710328 0.0009 GCT (A) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) 37 1 -8.0038078071 0.0434 GAC (D) GAC (D) GAT (D) GAC (D) GAC (D) GAC (D) GAC (D) 38 1 -19.2209541782 0.0000 AGA (R) AGA (R) GAA (E) GAA (E) CAA (Q) CAA (Q) CAA (Q) 39 1 -4.2784689093 1.8023 TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) 40 1 -4.5413001563 1.3857 GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) 41 1 -4.5300265454 1.4015 ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) 42 1 -4.6476460878 1.2459 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) 43 2 -4.9562014725 0.9152 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) 44 2 -4.6725375419 1.2153 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) 45 1 -13.9526908087 0.0001 CGC (R) CGC (R) CGC (R) CGC (R) CAC (H) CAC (H) CAC (H) 46 1 -7.7072272546 0.0584 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAT (Y) TAT (Y) 47 1 -8.6619538016 0.0225 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAC (N) 48 1 -7.6386523715 0.0626 GAT (D) GAT (D) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) 49 1 -7.6180808245 0.0639 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AGA (R) AGA (R) 50 1 -4.7949680407 1.0753 ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) 51 2 -5.3234573070 0.6339 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) 52 2 -4.3494722978 1.6788 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) 53 1 -7.9306430266 0.0467 AAT (N) AAT (N) AAT (N) GAT (D) AAT (N) AAT (N) AAT (N) 54 1 -4.6439287862 1.2506 CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) 55 1 -10.8202341235 0.0026 TTA (L) TTA (L) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) 56 1 -5.0984488784 0.7938 TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) 57 1 -4.6812000239 1.2048 TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) 58 1 -12.7247989627 0.0004 AGT (S) AAT (N) AAT (N) AGT (S) AAT (N) AAT (N) AAT (N) 59 3 -4.7045988601 1.1770 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) 60 1 -11.0532635455 0.0021 GAT (D) GAT (D) AAT (N) AAC (N) GAT (D) GAT (D) GAT (D) 61 1 -7.7553120801 0.0557 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) GAC (D) GAC (D) 62 1 -12.8896050389 0.0003 GCT (A) GCC (A) GCT (A) GCT (A) GCT (A) ACT (T) ACT (T) 63 1 -15.5069596712 0.0000 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) CAA (Q) GAA (E) 64 1 -8.1360516790 0.0381 GTA (V) GTA (V) GTA (V) GTA (V) GTA (V) GTG (V) GTG (V) 65 1 -13.5299247810 0.0002 GCT (A) GCT (A) GCT (A) GCT (A) ACT (T) GCC (A) GCC (A) 66 1 -4.6436582159 1.2509 GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) 67 1 -21.1344087505 0.0000 CGT (R) CGC (R) AGT (S) AGT (S) AGT (S) CGT (R) CGC (R) 68 1 -8.6870212211 0.0219 ATT (I) ATT (I) ATT (I) GTT (V) ATT (I) ATT (I) ATT (I) 69 1 -16.1125630985 0.0000 AGA (R) AGA (R) CGA (R) CGA (R) AGA (R) AGA (R) AGG (R) 70 1 -4.7433920156 1.1322 GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) 71 1 -11.8747575648 0.0009 AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AAA (K) AAA (K) 72 1 -18.5148919180 0.0000 AAT (N) AAT (N) AAG (K) AAT (N) AAT (N) GCT (A) GCT (A) 73 1 -13.9739064280 0.0001 CGT (R) CGT (R) CAC (H) CAC (H) CAC (H) CAT (H) CAT (H) 74 1 -8.4292988369 0.0284 AGA (R) AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AGA (R) 75 1 -12.0273836865 0.0008 GTC (V) CTC (L) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) 76 1 -10.1811649098 0.0049 CGT (R) CGT (R) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) 77 1 -8.5983529672 0.0240 TAT (Y) TAT (Y) TAT (Y) TAC (Y) TAT (Y) TAT (Y) TAT (Y) 78 1 -9.0044467619 0.0160 GTT (V) ATT (I) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) 79 1 -13.1118009094 0.0003 CAA (Q) CAA (Q) GAA (E) AAA (K) CAA (Q) CAA (Q) CAA (Q) 80 1 -4.1980256429 1.9533 GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) 81 1 -16.7711131668 0.0000 GTG (V) GTA (V) GTA (V) GTG (V) GTG (V) GTA (V) GTA (V) 2 1 2 -4.4631960839 1.4983 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) 2 1 -9.5051314395 0.0097 GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) GTC (V) GTC (V) 3 1 -9.7022223614 0.0079 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTC (F) TTT (F) 4 1 -4.2039287045 1.9418 GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) 5 2 -4.5556198392 1.3660 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) 6 7 -4.3823933327 1.6244 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) 7 2 -4.4321358567 1.5456 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) 8 3 -5.0765675735 0.8114 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) 9 3 -4.7615736591 1.1118 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) 10 1 -4.3184560927 1.7317 AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) 11 2 -4.5084089014 1.4321 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) 12 2 -5.4399559761 0.5642 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) 13 2 -4.2373003501 1.8781 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) 14 1 -10.9655163954 0.0022 AGA (R) AGA (R) AAA (K) AAA (K) AGA (R) AGG (R) AGG (R) 15 1 -16.0576801224 0.0000 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) CTT (L) TTT (F) 16 5 -4.3016164401 1.7611 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) 17 1 -18.1074279846 0.0000 ATG (M) ATG (M) CTG (L) CTG (L) CTG (L) ATG (M) CTG (L) 18 4 -4.1086794471 2.1358 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) 19 3 -4.4725278080 1.4844 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) 20 2 -4.5810712480 1.3317 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) 21 1 -8.2006676359 0.0357 AGG (R) AGG (R) AAG (K) AAG (K) AGG (R) AGG (R) AGG (R) 22 1 -8.6032803791 0.0239 ATC (I) ATC (I) GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) 23 3 -4.4856451080 1.4650 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) 24 1 -5.2057180047 0.7131 CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) 25 5 -4.6403399094 1.2551 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) 26 4 -4.4201673653 1.5642 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) 27 5 -4.5973665349 1.3102 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) 28 1 -9.7392749110 0.0077 ATG (M) ATG (M) GTG (V) GTG (V) GTG (V) ATG (M) ATG (M) 29 1 -4.2139743758 1.9224 AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) 30 1 -19.3632917534 0.0000 GGT (G) GGT (G) GGT (G) GGT (G) AAT (N) GAC (D) GAT (D) 31 1 -9.2797457778 0.0121 TAC (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) 32 2 -4.6757517792 1.2114 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) 33 1 -25.8812555227 0.0000 CGA (R) CGA (R) GAC (D) GAA (E) CAA (Q) CGT (R) CGT (R) 34 3 -4.4744739440 1.4815 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) 35 2 -4.1412559724 2.0674 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) 36 1 -11.8290647008 0.0009 GCT (A) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) 37 1 -8.0038170642 0.0434 GAC (D) GAC (D) GAT (D) GAC (D) GAC (D) GAC (D) GAC (D) 38 1 -19.2209226010 0.0000 AGA (R) AGA (R) GAA (E) GAA (E) CAA (Q) CAA (Q) CAA (Q) 39 1 -4.2784711487 1.8023 TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) 40 1 -4.5413014475 1.3857 GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) 41 1 -4.5300288594 1.4014 ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) 42 1 -4.6476474833 1.2459 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) 43 2 -4.9562019622 0.9151 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) 44 2 -4.6725389296 1.2153 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) 45 1 -13.9526618018 0.0001 CGC (R) CGC (R) CGC (R) CGC (R) CAC (H) CAC (H) CAC (H) 46 1 -7.7072324162 0.0584 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAT (Y) TAT (Y) 47 1 -8.6619636890 0.0225 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAC (N) 48 1 -7.6386352162 0.0626 GAT (D) GAT (D) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) 49 1 -7.6180754543 0.0639 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AGA (R) AGA (R) 50 1 -4.7949692808 1.0753 ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) 51 2 -5.3234581195 0.6339 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) 52 2 -4.3494743162 1.6788 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) 53 1 -7.9306463733 0.0467 AAT (N) AAT (N) AAT (N) GAT (D) AAT (N) AAT (N) AAT (N) 54 1 -4.6439311725 1.2506 CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) 55 1 -10.8202230892 0.0026 TTA (L) TTA (L) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) 56 1 -5.0984494878 0.7938 TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) 57 1 -4.6812015121 1.2048 TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) 58 1 -12.7247851075 0.0004 AGT (S) AAT (N) AAT (N) AGT (S) AAT (N) AAT (N) AAT (N) 59 3 -4.7045995761 1.1770 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) 60 1 -11.0532674855 0.0021 GAT (D) GAT (D) AAT (N) AAC (N) GAT (D) GAT (D) GAT (D) 61 1 -7.7553062341 0.0557 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) GAC (D) GAC (D) 62 1 -12.8895989932 0.0003 GCT (A) GCC (A) GCT (A) GCT (A) GCT (A) ACT (T) ACT (T) 63 1 -15.5069647657 0.0000 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) CAA (Q) GAA (E) 64 1 -8.1360564354 0.0381 GTA (V) GTA (V) GTA (V) GTA (V) GTA (V) GTG (V) GTG (V) 65 1 -13.5299179395 0.0002 GCT (A) GCT (A) GCT (A) GCT (A) ACT (T) GCC (A) GCC (A) 66 1 -4.6436592953 1.2509 GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) 67 1 -21.1344217788 0.0000 CGT (R) CGC (R) AGT (S) AGT (S) AGT (S) CGT (R) CGC (R) 68 1 -8.6870227601 0.0219 ATT (I) ATT (I) ATT (I) GTT (V) ATT (I) ATT (I) ATT (I) 69 1 -16.1125651833 0.0000 AGA (R) AGA (R) CGA (R) CGA (R) AGA (R) AGA (R) AGG (R) 70 1 -4.7433927068 1.1322 GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) 71 1 -11.8747461571 0.0009 AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AAA (K) AAA (K) 72 1 -18.5148907665 0.0000 AAT (N) AAT (N) AAG (K) AAT (N) AAT (N) GCT (A) GCT (A) 73 1 -13.9738939870 0.0001 CGT (R) CGT (R) CAC (H) CAC (H) CAC (H) CAT (H) CAT (H) 74 1 -8.4293011794 0.0284 AGA (R) AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AGA (R) 75 1 -12.0273822050 0.0008 GTC (V) CTC (L) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) 76 1 -10.1811554378 0.0049 CGT (R) CGT (R) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) 77 1 -8.5983668126 0.0240 TAT (Y) TAT (Y) TAT (Y) TAC (Y) TAT (Y) TAT (Y) TAT (Y) 78 1 -9.0044370152 0.0160 GTT (V) ATT (I) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) 79 1 -13.1117968019 0.0003 CAA (Q) CAA (Q) GAA (E) AAA (K) CAA (Q) CAA (Q) CAA (Q) 80 1 -4.1980290700 1.9533 GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) 81 1 -16.7711243929 0.0000 GTG (V) GTA (V) GTA (V) GTG (V) GTG (V) GTA (V) GTA (V) Bio-Tools-Phylo-PAML-1.7.3/t/data/aaml_pairwise.mlc0000644000175000017500000000626513316145226022653 0ustar carandraugcarandraugAAML (in paml 3.13, August 2002) abglobin.aa Model: Empirical_F (wag.dat) ns = 5 ls = 285 # site patterns = 126 16 21 10 1 1 10 17 1 1 2 1 1 3 1 13 1 2 1 1 5 2 1 5 15 1 1 5 1 10 1 1 7 10 1 14 1 1 1 1 1 3 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 4 1 4 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 human VLSPADKTNV AAWGGAHAEY GAEALERMFL SPTPHFLSHA QVKGKADTNV AVDMNALANL CLALPAEFAV LSSTPESAVT ALGNVDEVQF ETPDVMGKLG ASDLANFTCR VLCVAHFEPV AAYVNK goat-cow ...A...S.. .....GN.A. .......... .......... ....E.A.K. GL.LGT.D.. S.C..ND... .N..A.A... .F.K...... ..A...N..D S.NMKD.A.K ..V..R..VL .DF..R rabbit .........I T..E.S.G.. ....V..... G.....FT.E .I.A.SE.K. GL.LG..T.. ..NH.S.... .N.SS..... .....E.... .SAN..N..A ..E.S..K.. ..I.S...Q. ...... rat ...AD....I NC...G.G.. .E...Q...A A..S.IV.P. ...A...AKA D.ELG..T.F ..CH.GD..M ....DAA..N ....P.D..Y DSASI...IN .N..K..H.. MII.G.L.CA ..F.S. marsupial ...D....H. .I...G..A. A....A.T.. ........P. .IQ....SQ. .L.LGTMK.. .I..SKDLE. F.A.S.NCI. TISQ..QTT. GS.G..SA.T SGEVK.YK.K IIIC.E.DEC V.WLH. Frequencies.. A R N D C Q E G H I L K M F P S T W Y V human 0.1263 0.0211 0.0351 0.0526 0.0105 0.0140 0.0421 0.0702 0.0632 0.0000 0.1263 0.0772 0.0105 0.0526 0.0491 0.0561 0.0561 0.0105 0.0211 0.1053 goat-cow 0.1193 0.0246 0.0421 0.0632 0.0070 0.0140 0.0386 0.0737 0.0526 0.0000 0.1298 0.0842 0.0105 0.0596 0.0351 0.0596 0.0526 0.0105 0.0175 0.1053 rabbit 0.0982 0.0211 0.0421 0.0386 0.0070 0.0175 0.0596 0.0702 0.0667 0.0140 0.1228 0.0842 0.0070 0.0561 0.0386 0.0737 0.0561 0.0105 0.0211 0.0947 rat 0.1193 0.0211 0.0386 0.0667 0.0175 0.0175 0.0316 0.0807 0.0667 0.0246 0.1123 0.0842 0.0140 0.0491 0.0386 0.0596 0.0456 0.0105 0.0211 0.0807 marsupial 0.1088 0.0175 0.0211 0.0561 0.0175 0.0281 0.0351 0.0702 0.0632 0.0281 0.1088 0.0842 0.0175 0.0491 0.0351 0.0737 0.0667 0.0140 0.0211 0.0842 Average 0.1144 0.0211 0.0358 0.0554 0.0119 0.0182 0.0414 0.0730 0.0625 0.0133 0.1200 0.0828 0.0119 0.0533 0.0393 0.0646 0.0554 0.0112 0.0204 0.0940 # constant sites: 170 (59.65%) ln Lmax (unconstrained) = -1189.106658 AA distances (raw proportions of different sites) human goat-cow 0.1439 rabbit 0.1368 0.1825 rat 0.2000 0.2351 0.2035 marsupial 0.2456 0.2561 0.2877 0.3123 ML distances of aa seqs. human goat-cow 0.1551 rabbit 0.1474 0.2020 rat 0.2267 0.2694 0.2306 marsupial 0.2870 0.3024 0.3392 0.3861 Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml43_nssites.mlc0000644000175000017500000002610113316145226023207 0ustar carandraugcarandraug seed used = 739250845 CODONML (in paml version 4.3, August 2009) abglobin.nuc Model: One dN/dS ratio for branches Codon frequency model: F3x4 Site-class models: ns = 5 ls = 285 Codon usage in sequences -------------------------------------------------------------------------------------------------- Phe TTT 5 8 3 3 6 | Ser TCT 4 2 6 7 6 | Tyr TAT 3 2 3 1 1 | Cys TGT 2 1 1 2 2 TTC 10 9 13 11 8 | TCC 6 7 7 3 8 | TAC 3 3 3 5 5 | TGC 1 1 1 3 3 Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 TTG 0 2 1 4 5 | TCG 0 1 0 0 2 | TAG 0 0 0 0 0 | Trp TGG 3 3 3 3 4 -------------------------------------------------------------------------------------------------- Leu CTT 1 1 0 1 3 | Pro CCT 7 2 4 7 3 | His CAT 2 4 4 5 6 | Arg CGT 1 2 1 2 1 CTC 5 4 4 4 7 | CCC 3 6 5 4 7 | CAC 16 11 15 14 12 | CGC 0 1 0 0 0 CTA 1 2 0 2 1 | CCA 2 0 1 0 0 | Gln CAA 0 0 0 0 1 | CGA 0 0 0 0 0 CTG 29 28 30 21 15 | CCG 2 2 1 0 0 | CAG 4 4 5 5 7 | CGG 1 0 1 0 0 -------------------------------------------------------------------------------------------------- Ile ATT 0 0 1 4 1 | Thr ACT 3 4 4 3 10 | Asn AAT 1 5 5 3 2 | Ser AGT 2 3 5 2 1 ATC 0 0 3 2 7 | ACC 12 11 12 9 9 | AAC 9 7 7 8 4 | AGC 4 4 3 5 3 ATA 0 0 0 1 0 | ACA 1 0 0 1 0 | Lys AAA 4 3 5 5 3 | Arg AGA 0 1 0 0 2 Met ATG 3 3 2 4 5 | ACG 0 0 0 0 0 | AAG 18 21 19 19 21 | AGG 4 3 4 4 2 -------------------------------------------------------------------------------------------------- Val GTT 5 5 4 4 6 | Ala GCT 8 11 8 13 10 | Asp GAT 5 8 1 11 6 | Gly GGT 5 4 5 6 10 GTC 4 6 2 4 3 | GCC 21 18 16 18 19 | GAC 10 10 10 8 10 | GGC 14 15 14 12 5 GTA 0 0 0 1 1 | GCA 0 1 1 3 2 | Glu GAA 2 2 7 4 4 | GGA 0 1 0 3 3 GTG 21 19 21 14 14 | GCG 7 4 3 0 0 | GAG 10 9 10 5 6 | GGG 1 1 1 2 2 -------------------------------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: human position 1: T:0.12982 C:0.25965 A:0.21404 G:0.39649 position 2: T:0.29474 C:0.26667 A:0.30526 G:0.13333 position 3: T:0.18947 C:0.41404 A:0.03509 G:0.36140 Average T:0.20468 C:0.31345 A:0.18480 G:0.29708 #2: goat-cow position 1: T:0.13684 C:0.23509 A:0.22807 G:0.40000 position 2: T:0.30526 C:0.24211 A:0.31228 G:0.14035 position 3: T:0.21754 C:0.39649 A:0.03509 G:0.35088 Average T:0.21988 C:0.29123 A:0.19181 G:0.29708 #3: rabbit position 1: T:0.14386 C:0.24912 A:0.24561 G:0.36140 position 2: T:0.29474 C:0.23860 A:0.32982 G:0.13684 position 3: T:0.19298 C:0.40351 A:0.04912 G:0.35439 Average T:0.21053 C:0.29708 A:0.20819 G:0.28421 #4: rat position 1: T:0.14737 C:0.22807 A:0.24561 G:0.37895 position 2: T:0.28070 C:0.23860 A:0.32632 G:0.15439 position 3: T:0.25965 C:0.38596 A:0.07018 G:0.28421 Average T:0.22924 C:0.28421 A:0.21404 G:0.27251 #5: marsupial position 1: T:0.17895 C:0.22105 A:0.24561 G:0.35439 position 2: T:0.28772 C:0.27018 A:0.30877 G:0.13333 position 3: T:0.25965 C:0.38596 A:0.06316 G:0.29123 Average T:0.24211 C:0.29240 A:0.20585 G:0.25965 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 25 | Ser S TCT 25 | Tyr Y TAT 10 | Cys C TGT 8 TTC 51 | TCC 31 | TAC 19 | TGC 9 Leu L TTA 0 | TCA 1 | *** * TAA 0 | *** * TGA 0 TTG 12 | TCG 3 | TAG 0 | Trp W TGG 16 ------------------------------------------------------------------------------ Leu L CTT 6 | Pro P CCT 23 | His H CAT 21 | Arg R CGT 7 CTC 24 | CCC 25 | CAC 68 | CGC 1 CTA 6 | CCA 3 | Gln Q CAA 1 | CGA 0 CTG 123 | CCG 5 | CAG 25 | CGG 2 ------------------------------------------------------------------------------ Ile I ATT 6 | Thr T ACT 24 | Asn N AAT 16 | Ser S AGT 13 ATC 12 | ACC 53 | AAC 35 | AGC 19 ATA 1 | ACA 2 | Lys K AAA 20 | Arg R AGA 3 Met M ATG 17 | ACG 0 | AAG 98 | AGG 17 ------------------------------------------------------------------------------ Val V GTT 24 | Ala A GCT 50 | Asp D GAT 31 | Gly G GGT 30 GTC 19 | GCC 92 | GAC 48 | GGC 60 GTA 2 | GCA 7 | Glu E GAA 19 | GGA 7 GTG 89 | GCG 14 | GAG 40 | GGG 7 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.14737 C:0.23860 A:0.23579 G:0.37825 position 2: T:0.29263 C:0.25123 A:0.31649 G:0.13965 position 3: T:0.22386 C:0.39719 A:0.05053 G:0.32842 Average T:0.22129 C:0.29567 A:0.20094 G:0.28211 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) human goat-cow 0.2507 (0.0863 0.3443) rabbit 0.2627 (0.0867 0.3301) 0.2943 (0.1054 0.3581) rat 0.2045 (0.1261 0.6164) 0.2462 (0.1493 0.6065) 0.2178 (0.1348 0.6187) marsupial 0.1902 (0.1931 1.0148) 0.1891 (0.1910 1.0099) 0.2184 (0.2111 0.9668) 0.2716 (0.2404 0.8852) Model 1: NearlyNeutral (2 categories) TREE # 1: (((3, 4), 1), 2, 5); MP score: 387 lnL(ntime: 7 np: 10): -2970.527521 +0.000000 6..7 7..8 8..3 8..4 7..1 6..2 6..5 0.081884 0.073268 0.252707 0.649536 0.215600 0.223230 1.401893 2.066843 0.826211 0.065970 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 2.89812 (((3: 0.252707, 4: 0.649536): 0.073268, 1: 0.215600): 0.081884, 2: 0.223230, 5: 1.401893); (((rabbit: 0.252707, rat: 0.649536): 0.073268, human: 0.215600): 0.081884, goat-cow: 0.223230, marsupial: 1.401893); Detailed output identifying parameters kappa (ts/tv) = 2.06684 dN/dS (w) for site classes (K=2) p: 0.82621 0.17379 w: 0.06597 1.00000 dN & dS for each branch branch t N S dN/dS dN dS N*dN S*dS 6..7 0.082 663.8 191.2 0.2283 0.0155 0.0681 10.3 13.0 7..8 0.073 663.8 191.2 0.2283 0.0139 0.0609 9.2 11.7 8..3 0.253 663.8 191.2 0.2283 0.0480 0.2101 31.8 40.2 8..4 0.650 663.8 191.2 0.2283 0.1233 0.5401 81.8 103.3 7..1 0.216 663.8 191.2 0.2283 0.0409 0.1793 27.2 34.3 6..2 0.223 663.8 191.2 0.2283 0.0424 0.1856 28.1 35.5 6..5 1.402 663.8 191.2 0.2283 0.2661 1.1656 176.6 222.9 Naive Empirical Bayes (NEB) analysis Time used: 0:08 Model 2: PositiveSelection (3 categories) TREE # 1: (((3, 4), 1), 2, 5); MP score: 387 lnL(ntime: 7 np: 12): -2965.809712 +0.000000 6..7 7..8 8..3 8..4 7..1 6..2 6..5 0.100782 0.089538 0.293059 0.801779 0.242098 0.264641 1.797878 2.181363 0.833468 0.136461 0.072723 6.285989 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 3.58978 (((3: 0.293059, 4: 0.801779): 0.089538, 1: 0.242098): 0.100782, 2: 0.264641, 5: 1.797878); (((rabbit: 0.293059, rat: 0.801779): 0.089538, human: 0.242098): 0.100782, goat-cow: 0.264641, marsupial: 1.797878); Detailed output identifying parameters kappa (ts/tv) = 2.18136 dN/dS (w) for site classes (K=3) p: 0.83347 0.13646 0.03007 w: 0.07272 1.00000 6.28599 dN & dS for each branch branch t N S dN/dS dN dS N*dN S*dS 6..7 0.101 662.3 192.7 0.3861 0.0247 0.0641 16.4 12.3 7..8 0.090 662.3 192.7 0.3861 0.0220 0.0569 14.6 11.0 8..3 0.293 662.3 192.7 0.3861 0.0719 0.1863 47.6 35.9 8..4 0.802 662.3 192.7 0.3861 0.1968 0.5096 130.3 98.2 7..1 0.242 662.3 192.7 0.3861 0.0594 0.1539 39.4 29.6 6..2 0.265 662.3 192.7 0.3861 0.0649 0.1682 43.0 32.4 6..5 1.798 662.3 192.7 0.3861 0.4412 1.1428 292.2 220.2 Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: human) Pr(w>1) post mean +- SE for w 35 S 0.643 4.400 111 A 0.736 4.890 115 A 0.785 5.151 131 S 0.704 4.722 144 P 0.794 5.198 215 A 0.799 5.225 226 T 0.560 3.962 264 P 0.971* 6.134 Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: human) Pr(w>1) post mean +- SE for w 35 S 0.634 4.600 +- 3.257 111 A 0.727 5.133 +- 3.164 115 A 0.779 5.538 +- 3.111 131 S 0.706 5.170 +- 3.273 144 P 0.781 5.485 +- 3.082 195 G 0.502 3.842 +- 3.253 215 A 0.788 5.577 +- 3.082 226 T 0.572 4.307 +- 3.325 264 P 0.964* 6.573 +- 2.443 The grid (see ternary graph for p0-p1) w0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950 w2: 1.500 2.500 3.500 4.500 5.500 6.500 7.500 8.500 9.500 10.500 Posterior on the grid w0: 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 w2: 0.006 0.033 0.085 0.129 0.147 0.146 0.135 0.121 0.106 0.092 Posterior for p0-p1 (see the ternary graph) 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.199 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.100 0.700 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.000 sum of density on p0-p1 = 1.000000 Time used: 0:26 Time used: 0:26 Bio-Tools-Phylo-PAML-1.7.3/t/data/yn00_45.mlc0000644000175000017500000007052413316145226021133 0ustar carandraugcarandraugYN00 examples/small_taxon_set.nuc ns = 9 ls = 475 Codon position x base (3x4) table for each sequence. Pdel181_DNA2 position 1: T:0.18105 C:0.19368 A:0.23579 G:0.38947 position 2: T:0.26526 C:0.23158 A:0.30105 G:0.20211 position 3: T:0.41895 C:0.15579 A:0.28211 G:0.14316 Pfre186_DNA2 position 1: T:0.18105 C:0.19368 A:0.23789 G:0.38737 position 2: T:0.26526 C:0.23158 A:0.30105 G:0.20211 position 3: T:0.41895 C:0.15579 A:0.28211 G:0.14316 Pgra187_DNA2 position 1: T:0.18105 C:0.19158 A:0.24000 G:0.38737 position 2: T:0.26316 C:0.23158 A:0.30105 G:0.20421 position 3: T:0.42105 C:0.15158 A:0.28632 G:0.14105 Phet26_DNA21 position 1: T:0.18105 C:0.19368 A:0.23368 G:0.39158 position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 position 3: T:0.41895 C:0.15789 A:0.28632 G:0.13684 Pmex37_DNA21 position 1: T:0.18105 C:0.19158 A:0.23789 G:0.38947 position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 position 3: T:0.41895 C:0.15789 A:0.28211 G:0.14105 Ptre197_DNA2 position 1: T:0.18105 C:0.19158 A:0.24000 G:0.38737 position 2: T:0.26316 C:0.23158 A:0.30105 G:0.20421 position 3: T:0.42316 C:0.15158 A:0.28421 G:0.14105 WHR1_DNA225 position 1: T:0.18105 C:0.19158 A:0.23579 G:0.39158 position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 position 3: T:0.41684 C:0.15579 A:0.28211 G:0.14526 YALD273_DNA5 position 1: T:0.18105 C:0.19368 A:0.23368 G:0.39158 position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 position 3: T:0.41895 C:0.15789 A:0.28632 G:0.13684 Pop_trich_ch position 1: T:0.18105 C:0.19368 A:0.23368 G:0.39158 position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 position 3: T:0.41895 C:0.15789 A:0.28632 G:0.13684 Average position 1: T:0.18105 C:0.19275 A:0.23649 G:0.38971 position 2: T:0.26480 C:0.23041 A:0.30105 G:0.20374 position 3: T:0.41942 C:0.15579 A:0.28421 G:0.14058 Codon usage for each species -------------------------------------------------------------------------------------------------------------- Phe TTT 14 14 14 14 14 14 | Ser TCT 6 6 6 6 6 6 | Tyr TAT 13 13 13 13 13 13 | Cys TGT 5 5 5 5 5 5 TTC 8 8 8 8 8 8 | TCC 4 4 4 4 4 4 | TAC 4 4 4 4 4 4 | TGC 3 3 3 3 3 3 Leu TTA 9 9 9 9 9 9 | TCA 1 1 1 1 1 1 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 TTG 10 10 10 10 10 10 | TCG 1 1 1 1 1 1 | TAG 0 0 0 0 0 0 | Trp TGG 8 8 8 8 8 8 -------------------------------------------------------------------------------------------------------------- Leu CTT 9 9 9 9 9 9 | Pro CCT 11 11 12 11 10 12 | His CAT 9 9 9 9 9 9 | Arg CGT 11 11 11 11 11 11 CTC 0 0 0 0 0 0 | CCC 6 6 5 6 6 5 | CAC 5 5 5 5 5 5 | CGC 5 5 5 5 5 5 CTA 9 9 9 10 9 9 | CCA 3 3 3 3 3 3 | Gln CAA 10 10 9 10 10 9 | CGA 6 6 6 6 6 6 CTG 4 4 4 3 4 4 | CCG 2 2 2 2 2 2 | CAG 2 2 2 2 2 2 | CGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------- Ile ATT 10 11 10 10 11 10 | Thr ACT 17 17 18 16 17 18 | Asn AAT 9 9 9 9 9 9 | Ser AGT 1 1 2 2 2 2 ATC 9 9 7 9 9 8 | ACC 8 8 8 8 8 8 | AAC 6 6 6 6 6 6 | AGC 3 3 3 3 3 3 ATA 1 1 4 2 1 3 | ACA 6 6 5 5 5 5 | Lys AAA 18 18 18 18 18 18 | Arg AGA 6 6 6 6 6 6 Met ATG 10 10 10 9 10 10 | ACG 1 1 1 1 1 1 | AAG 6 6 6 6 6 6 | AGG 1 1 1 1 1 1 -------------------------------------------------------------------------------------------------------------- Val GTT 15 14 14 15 14 14 | Ala GCT 24 24 23 24 24 24 | Asp GAT 22 22 22 22 22 22 | Gly GGT 23 23 23 23 23 23 GTC 1 1 1 1 1 1 | GCC 5 5 5 5 5 4 | GAC 5 5 6 6 6 6 | GGC 2 2 2 2 2 2 GTA 13 13 12 13 13 12 | GCA 15 15 16 16 16 16 | Glu GAA 24 24 25 24 24 25 | GGA 13 13 13 13 13 13 GTG 4 4 4 4 4 4 | GCG 0 0 0 0 0 0 | GAG 10 10 9 9 9 9 | GGG 9 9 9 9 9 9 -------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------- Phe TTT 14 14 14 | Ser TCT 5 6 6 | Tyr TAT 13 13 13 | Cys TGT 5 5 5 TTC 8 8 8 | TCC 5 4 4 | TAC 4 4 4 | TGC 3 3 3 Leu TTA 9 9 9 | TCA 1 1 1 | *** TAA 0 0 0 | *** TGA 0 0 0 TTG 10 10 10 | TCG 1 1 1 | TAG 0 0 0 | Trp TGG 8 8 8 -------------------------------------------------------------------------- Leu CTT 9 9 9 | Pro CCT 10 11 11 | His CAT 9 9 9 | Arg CGT 11 11 11 CTC 0 0 0 | CCC 6 6 6 | CAC 5 5 5 | CGC 5 5 5 CTA 9 10 10 | CCA 3 3 3 | Gln CAA 10 10 10 | CGA 6 6 6 CTG 4 3 3 | CCG 2 2 2 | CAG 2 2 2 | CGG 0 0 0 -------------------------------------------------------------------------- Ile ATT 10 10 10 | Thr ACT 17 16 16 | Asn AAT 9 9 9 | Ser AGT 2 2 2 ATC 8 9 9 | ACC 8 8 8 | AAC 6 6 6 | AGC 3 3 3 ATA 2 2 2 | ACA 5 5 5 | Lys AAA 18 18 18 | Arg AGA 6 6 6 Met ATG 10 9 9 | ACG 1 1 1 | AAG 6 6 6 | AGG 1 1 1 -------------------------------------------------------------------------- Val GTT 15 15 15 | Ala GCT 24 24 24 | Asp GAT 22 22 22 | Gly GGT 23 23 23 GTC 1 1 1 | GCC 5 5 5 | GAC 5 6 6 | GGC 2 2 2 GTA 13 13 13 | GCA 15 16 16 | Glu GAA 24 24 24 | GGA 13 13 13 GTG 4 4 4 | GCG 1 0 0 | GAG 10 9 9 | GGG 9 9 9 -------------------------------------------------------------------------- Sums -------------------------------------------------- Phe TTT 126 | Ser TCT 53 | Tyr TAT 117 | Cys TGT 45 TTC 72 | TCC 37 | TAC 36 | TGC 27 Leu TTA 81 | TCA 9 | *** TAA 0 | *** TGA 0 TTG 90 | TCG 9 | TAG 0 | Trp TGG 72 -------------------------------------------------- Leu CTT 81 | Pro CCT 99 | His CAT 81 | Arg CGT 99 CTC 0 | CCC 52 | CAC 45 | CGC 45 CTA 84 | CCA 27 | Gln CAA 88 | CGA 54 CTG 33 | CCG 18 | CAG 18 | CGG 0 -------------------------------------------------- Ile ATT 92 | Thr ACT 152 | Asn AAT 81 | Ser AGT 16 ATC 77 | ACC 72 | AAC 54 | AGC 27 ATA 18 | ACA 47 | Lys AAA 162 | Arg AGA 54 Met ATG 87 | ACG 9 | AAG 54 | AGG 9 -------------------------------------------------- Val GTT 131 | Ala GCT 215 | Asp GAT 198 | Gly GGT 207 GTC 9 | GCC 44 | GAC 51 | GGC 18 GTA 115 | GCA 141 | Glu GAA 218 | GGA 117 GTG 36 | GCG 1 | GAG 84 | GGG 81 -------------------------------------------------- (A) Nei-Gojobori (1986) method Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later ML. analysis. Use runmode = -2 for ML pairwise comparison.) Pdel181_DNA2 Pfre186_DNA2 -1.0000 (0.0009 0.0000) Pgra187_DNA2 1.0623 (0.0093 0.0088) 1.1684 (0.0102 0.0088) Phet26_DNA21 1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117) Pmex37_DNA21 -1.0000 (0.0046 0.0000)-1.0000 (0.0037 0.0000) 0.9534 (0.0084 0.0088) 0.9555 (0.0028 0.0029) Ptre197_DNA2 1.5965 (0.0093 0.0058) 1.7561 (0.0102 0.0058) 0.0000 (0.0000 0.0088) 0.6357 (0.0056 0.0088) 1.4328 (0.0084 0.0058) WHR1_DNA225 0.7964 (0.0046 0.0058) 0.9557 (0.0056 0.0058) 0.4430 (0.0065 0.0147) 0.3175 (0.0028 0.0088) 0.6354 (0.0037 0.0058) 0.5548 (0.0065 0.0117) YALD273_DNA5 1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117)-1.0000 (0.0000 0.0000) 0.9555 (0.0028 0.0029) 0.6357 (0.0056 0.0088) 0.3175 (0.0028 0.0088) Pop_trich_ch 1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117)-1.0000 (0.0000 0.0000) 0.9555 (0.0028 0.0029) 0.6357 (0.0056 0.0088) 0.3175 (0.0028 0.0088)-1.0000 (0.0000 0.0000) (B) Yang & Nielsen (2000) method Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17:32-43 (equal weighting of pathways) seq. seq. S N t kappa omega dN +- SE dS +- SE 2 1 337.9 1087.1 0.0021 4.2358 99.0000 0.0009 +- 0.0009 -0.0000 +- 0.0000 3 1 335.1 1089.9 0.0276 4.2358 1.0246 0.0092 +- 0.0029 0.0090 +- 0.0052 3 2 334.8 1090.2 0.0297 4.2358 1.1268 0.0102 +- 0.0031 0.0090 +- 0.0052 4 1 337.9 1087.1 0.0106 4.2358 1.2441 0.0037 +- 0.0018 0.0030 +- 0.0030 4 2 337.6 1087.4 0.0127 4.2358 1.5546 0.0046 +- 0.0021 0.0030 +- 0.0030 4 3 334.8 1090.2 0.0212 4.2358 0.4581 0.0055 +- 0.0023 0.0121 +- 0.0061 5 1 338.1 1086.9 0.0106 4.2358 99.0000 0.0046 +- 0.0021 -0.0000 +- 0.0000 5 2 337.8 1087.2 0.0084 4.2358 99.0000 0.0037 +- 0.0018 -0.0000 +- 0.0000 5 3 335.0 1090.0 0.0254 4.2358 0.9214 0.0083 +- 0.0028 0.0090 +- 0.0052 5 4 337.8 1087.2 0.0084 4.2358 0.9322 0.0028 +- 0.0016 0.0030 +- 0.0030 6 1 334.8 1090.2 0.0254 4.2358 1.5397 0.0092 +- 0.0029 0.0060 +- 0.0042 6 2 334.5 1090.5 0.0276 4.2358 1.6932 0.0102 +- 0.0031 0.0060 +- 0.0042 6 3 331.7 1093.3 0.0064 4.2358 0.0000 -0.0000 +- 0.0000 0.0091 +- 0.0053 6 4 334.5 1090.5 0.0190 4.2358 0.6124 0.0055 +- 0.0023 0.0090 +- 0.0052 6 5 334.7 1090.3 0.0233 4.2358 1.3847 0.0083 +- 0.0028 0.0060 +- 0.0042 7 1 338.8 1086.2 0.0148 4.2358 0.7790 0.0046 +- 0.0021 0.0059 +- 0.0042 7 2 338.5 1086.5 0.0169 4.2358 0.9344 0.0055 +- 0.0023 0.0059 +- 0.0042 7 3 335.7 1089.3 0.0255 4.2358 0.4278 0.0065 +- 0.0024 0.0151 +- 0.0068 7 4 338.5 1086.5 0.0127 4.2358 0.3104 0.0028 +- 0.0016 0.0089 +- 0.0052 7 5 338.7 1086.3 0.0127 4.2358 0.6226 0.0037 +- 0.0018 0.0059 +- 0.0042 7 6 335.4 1089.6 0.0233 4.2358 0.5368 0.0065 +- 0.0024 0.0120 +- 0.0060 8 1 337.9 1087.1 0.0106 4.2358 1.2441 0.0037 +- 0.0018 0.0030 +- 0.0030 8 2 337.6 1087.4 0.0127 4.2358 1.5546 0.0046 +- 0.0021 0.0030 +- 0.0030 8 3 334.8 1090.2 0.0212 4.2358 0.4581 0.0055 +- 0.0023 0.0121 +- 0.0061 8 4 337.6 1087.4 -0.0000 4.2358 99.0000 -0.0000 +- 0.0000 -0.0000 +- 0.0000 8 5 337.8 1087.2 0.0084 4.2358 0.9322 0.0028 +- 0.0016 0.0030 +- 0.0030 8 6 334.5 1090.5 0.0190 4.2358 0.6124 0.0055 +- 0.0023 0.0090 +- 0.0052 8 7 338.5 1086.5 0.0127 4.2358 0.3104 0.0028 +- 0.0016 0.0089 +- 0.0052 9 1 337.9 1087.1 0.0106 4.2358 1.2441 0.0037 +- 0.0018 0.0030 +- 0.0030 9 2 337.6 1087.4 0.0127 4.2358 1.5546 0.0046 +- 0.0021 0.0030 +- 0.0030 9 3 334.8 1090.2 0.0212 4.2358 0.4581 0.0055 +- 0.0023 0.0121 +- 0.0061 9 4 337.6 1087.4 -0.0000 4.2358 99.0000 -0.0000 +- 0.0000 -0.0000 +- 0.0000 9 5 337.8 1087.2 0.0084 4.2358 0.9322 0.0028 +- 0.0016 0.0030 +- 0.0030 9 6 334.5 1090.5 0.0190 4.2358 0.6124 0.0055 +- 0.0023 0.0090 +- 0.0052 9 7 338.5 1086.5 0.0127 4.2358 0.3104 0.0028 +- 0.0016 0.0089 +- 0.0052 9 8 337.6 1087.4 -0.0000 4.2358 99.0000 -0.0000 +- 0.0000 -0.0000 +- 0.0000 (C) LWL85, LPB93 & LWLm methods Li W.-H., C.-I. Wu, Luo (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2: 150-174. Li W-H (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36:96-99 Pamilo P, Bianchi NO (1993) Evolution of the Zfx and Zfy genes - rates and interdependence between the genes. Mol. Biol. Evol. 10:271-281 Yang Z (2006) Computational Molecular Evolution. Oxford University Press, Oxford. Eqs. 2.12 & 2.13 2 (Pfre186_DNA2) vs. 1 (Pdel181_DNA2) L(i): 923.0 268.5 233.5 sum= 1425.0 Ns(i): 1.0000 0.0000 0.0000 sum= 1.0000 Nv(i): 0.0000 0.0000 0.0000 sum= 0.0000 A(i): 0.0011 0.0000 0.0000 B(i): -0.0000 -0.0000 -0.0000 LWL85: dS = 0.0000 dN = 0.0009 w = inf S = 323.0 N = 1102.0 LWL85m: dS = nan dN = nan w = nan S = nan N = nan (rho = nan) LPB93: dS = 0.0000 dN = 0.0011 w = inf 3 (Pgra187_DNA2) vs. 1 (Pdel181_DNA2) L(i): 923.0 269.0 233.0 sum= 1425.0 Ns(i): 5.5000 1.5000 1.0000 sum= 8.0000 Nv(i): 2.5000 2.5000 0.0000 sum= 5.0000 A(i): 0.0060 0.0056 0.0043 B(i): 0.0027 0.0094 -0.0000 LWL85: dS = 0.0078 dN = 0.0096 w = 1.2280 S = 322.7 N = 1102.3 LWL85m: dS = 0.0050 dN = 0.0115 w = 2.2818 S = 502.0 N = 923.0 (rho = 1.000) LPB93: dS = 0.0050 dN = 0.0102 w = 2.0369 3 (Pgra187_DNA2) vs. 2 (Pfre186_DNA2) L(i): 923.0 269.5 232.5 sum= 1425.0 Ns(i): 6.5000 1.5000 1.0000 sum= 9.0000 Nv(i): 2.5000 2.5000 0.0000 sum= 5.0000 A(i): 0.0071 0.0056 0.0043 B(i): 0.0027 0.0094 -0.0000 LWL85: dS = 0.0078 dN = 0.0105 w = 1.3442 S = 322.3 N = 1102.7 LWL85m: dS = 0.0050 dN = 0.0126 w = 2.5010 S = 502.0 N = 923.0 (rho = 1.000) LPB93: dS = 0.0050 dN = 0.0113 w = 2.2557 4 (Phet26_DNA21) vs. 1 (Pdel181_DNA2) L(i): 922.5 269.0 233.5 sum= 1425.0 Ns(i): 1.5000 0.5000 1.0000 sum= 3.0000 Nv(i): 1.0000 1.0000 0.0000 sum= 2.0000 A(i): 0.0016 0.0019 0.0043 B(i): 0.0011 0.0037 -0.0000 LWL85: dS = 0.0047 dN = 0.0032 w = 0.6832 S = 323.2 N = 1101.8 LWL85m: dS = 0.0030 dN = 0.0038 w = 1.2689 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0030 dN = 0.0033 w = 1.1052 4 (Phet26_DNA21) vs. 2 (Pfre186_DNA2) L(i): 922.5 269.5 233.0 sum= 1425.0 Ns(i): 2.5000 0.5000 1.0000 sum= 4.0000 Nv(i): 1.0000 1.0000 0.0000 sum= 2.0000 A(i): 0.0027 0.0019 0.0043 B(i): 0.0011 0.0037 -0.0000 LWL85: dS = 0.0047 dN = 0.0041 w = 0.8779 S = 322.8 N = 1102.2 LWL85m: dS = 0.0030 dN = 0.0049 w = 1.6325 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0030 dN = 0.0044 w = 1.4686 4 (Phet26_DNA21) vs. 3 (Pgra187_DNA2) L(i): 922.5 270.0 232.5 sum= 1425.0 Ns(i): 4.0000 1.0000 2.0000 sum= 7.0000 Nv(i): 1.5000 1.5000 0.0000 sum= 3.0000 A(i): 0.0044 0.0037 0.0087 B(i): 0.0016 0.0056 -0.0000 LWL85: dS = 0.0094 dN = 0.0064 w = 0.6803 S = 322.5 N = 1102.5 LWL85m: dS = 0.0060 dN = 0.0076 w = 1.2668 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0060 dN = 0.0069 w = 1.1440 5 (Pmex37_DNA21) vs. 1 (Pdel181_DNA2) L(i): 923.0 269.0 233.0 sum= 1425.0 Ns(i): 2.0000 0.0000 0.0000 sum= 2.0000 Nv(i): 2.0000 1.0000 0.0000 sum= 3.0000 A(i): 0.0022 -0.0000 0.0000 B(i): 0.0022 0.0037 -0.0000 LWL85: dS = -0.0000 dN = 0.0046 w =-1568.0041 S = 322.7 N = 1102.3 LWL85m: dS = nan dN = nan w = nan S = nan N = nan (rho = nan) LPB93: dS = -0.0000 dN = 0.0047 w =-2519.1394 5 (Pmex37_DNA21) vs. 2 (Pfre186_DNA2) L(i): 923.0 269.5 232.5 sum= 1425.0 Ns(i): 1.0000 0.0000 0.0000 sum= 1.0000 Nv(i): 2.0000 1.0000 0.0000 sum= 3.0000 A(i): 0.0011 -0.0000 0.0000 B(i): 0.0022 0.0037 -0.0000 LWL85: dS = -0.0000 dN = 0.0036 w =-1254.3509 S = 322.3 N = 1102.7 LWL85m: dS = nan dN = nan w = nan S = nan N = nan (rho = nan) LPB93: dS = -0.0000 dN = 0.0036 w =-1938.1612 5 (Pmex37_DNA21) vs. 3 (Pgra187_DNA2) L(i): 923.0 270.0 232.0 sum= 1425.0 Ns(i): 5.5000 1.5000 1.0000 sum= 8.0000 Nv(i): 2.5000 1.5000 0.0000 sum= 4.0000 A(i): 0.0060 0.0056 0.0043 B(i): 0.0027 0.0056 -0.0000 LWL85: dS = 0.0078 dN = 0.0087 w = 1.1081 S = 322.0 N = 1103.0 LWL85m: dS = 0.0050 dN = 0.0104 w = 2.0644 S = 502.0 N = 923.0 (rho = 1.000) LPB93: dS = 0.0050 dN = 0.0094 w = 1.8682 5 (Pmex37_DNA21) vs. 4 (Phet26_DNA21) L(i): 922.5 270.0 232.5 sum= 1425.0 Ns(i): 1.5000 0.5000 1.0000 sum= 3.0000 Nv(i): 1.0000 0.0000 0.0000 sum= 1.0000 A(i): 0.0016 0.0019 0.0043 B(i): 0.0011 -0.0000 -0.0000 LWL85: dS = 0.0047 dN = 0.0023 w = 0.4868 S = 322.5 N = 1102.5 LWL85m: dS = 0.0030 dN = 0.0027 w = 0.9065 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0030 dN = 0.0025 w = 0.8244 6 (Ptre197_DNA2) vs. 1 (Pdel181_DNA2) L(i): 923.0 269.0 233.0 sum= 1425.0 Ns(i): 5.5000 0.5000 2.0000 sum= 8.0000 Nv(i): 2.5000 1.5000 0.0000 sum= 4.0000 A(i): 0.0060 0.0019 0.0087 B(i): 0.0027 0.0056 -0.0000 LWL85: dS = 0.0078 dN = 0.0087 w = 1.1111 S = 322.7 N = 1102.3 LWL85m: dS = 0.0050 dN = 0.0104 w = 2.0645 S = 502.0 N = 923.0 (rho = 1.000) LPB93: dS = 0.0050 dN = 0.0094 w = 1.8688 6 (Ptre197_DNA2) vs. 2 (Pfre186_DNA2) L(i): 923.0 269.5 232.5 sum= 1425.0 Ns(i): 6.5000 0.5000 2.0000 sum= 9.0000 Nv(i): 2.5000 1.5000 0.0000 sum= 4.0000 A(i): 0.0071 0.0019 0.0087 B(i): 0.0027 0.0056 -0.0000 LWL85: dS = 0.0078 dN = 0.0096 w = 1.2275 S = 322.3 N = 1102.7 LWL85m: dS = 0.0050 dN = 0.0115 w = 2.2838 S = 502.0 N = 923.0 (rho = 1.000) LPB93: dS = 0.0050 dN = 0.0105 w = 2.0879 6 (Ptre197_DNA2) vs. 3 (Pgra187_DNA2) L(i): 923.0 270.0 232.0 sum= 1425.0 Ns(i): 0.0000 1.0000 1.0000 sum= 2.0000 Nv(i): 0.0000 1.0000 0.0000 sum= 1.0000 A(i): 0.0000 0.0037 0.0043 B(i): -0.0000 0.0037 -0.0000 LWL85: dS = 0.0062 dN = 0.0009 w = 0.1457 S = 322.0 N = 1103.0 LWL85m: dS = 0.0040 dN = 0.0011 w = 0.2715 S = 502.0 N = 923.0 (rho = 1.000) LPB93: dS = 0.0040 dN = 0.0008 w = 0.2100 6 (Ptre197_DNA2) vs. 4 (Phet26_DNA21) L(i): 922.5 270.0 232.5 sum= 1425.0 Ns(i): 4.0000 0.0000 3.0000 sum= 7.0000 Nv(i): 1.5000 0.5000 0.0000 sum= 2.0000 A(i): 0.0044 -0.0000 0.0131 B(i): 0.0016 0.0019 -0.0000 LWL85: dS = 0.0094 dN = 0.0055 w = 0.5801 S = 322.5 N = 1102.5 LWL85m: dS = 0.0060 dN = 0.0065 w = 1.0802 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0060 dN = 0.0060 w = 0.9989 6 (Ptre197_DNA2) vs. 5 (Pmex37_DNA21) L(i): 923.0 270.0 232.0 sum= 1425.0 Ns(i): 5.5000 0.5000 2.0000 sum= 8.0000 Nv(i): 2.5000 0.5000 0.0000 sum= 3.0000 A(i): 0.0060 0.0019 0.0087 B(i): 0.0027 0.0019 -0.0000 LWL85: dS = 0.0078 dN = 0.0078 w = 0.9913 S = 322.0 N = 1103.0 LWL85m: dS = 0.0050 dN = 0.0093 w = 1.8469 S = 502.0 N = 923.0 (rho = 1.000) LPB93: dS = 0.0050 dN = 0.0085 w = 1.6999 7 (WHR1_DNA225) vs. 1 (Pdel181_DNA2) L(i): 923.0 268.5 233.5 sum= 1425.0 Ns(i): 1.5000 0.5000 2.0000 sum= 4.0000 Nv(i): 2.5000 0.5000 0.0000 sum= 3.0000 A(i): 0.0016 0.0019 0.0086 B(i): 0.0027 0.0019 -0.0000 LWL85: dS = 0.0078 dN = 0.0041 w = 0.5251 S = 323.0 N = 1102.0 LWL85m: dS = 0.0050 dN = 0.0049 w = 0.9743 S = 502.0 N = 923.0 (rho = 1.000) LPB93: dS = 0.0050 dN = 0.0042 w = 0.8280 7 (WHR1_DNA225) vs. 2 (Pfre186_DNA2) L(i): 923.0 269.0 233.0 sum= 1425.0 Ns(i): 2.5000 0.5000 2.0000 sum= 5.0000 Nv(i): 2.5000 0.5000 0.0000 sum= 3.0000 A(i): 0.0027 0.0019 0.0087 B(i): 0.0027 0.0019 -0.0000 LWL85: dS = 0.0078 dN = 0.0050 w = 0.6414 S = 322.7 N = 1102.3 LWL85m: dS = 0.0050 dN = 0.0060 w = 1.1918 S = 502.0 N = 923.0 (rho = 1.000) LPB93: dS = 0.0050 dN = 0.0052 w = 1.0452 7 (WHR1_DNA225) vs. 3 (Pgra187_DNA2) L(i): 923.0 269.5 232.5 sum= 1425.0 Ns(i): 4.0000 1.0000 3.0000 sum= 8.0000 Nv(i): 2.0000 2.0000 0.0000 sum= 4.0000 A(i): 0.0044 0.0037 0.0131 B(i): 0.0022 0.0075 -0.0000 LWL85: dS = 0.0126 dN = 0.0073 w = 0.5811 S = 322.3 N = 1102.7 LWL85m: dS = 0.0081 dN = 0.0087 w = 1.0811 S = 502.0 N = 923.0 (rho = 1.000) LPB93: dS = 0.0081 dN = 0.0077 w = 0.9591 7 (WHR1_DNA225) vs. 4 (Phet26_DNA21) L(i): 922.5 269.5 233.0 sum= 1425.0 Ns(i): 0.0000 0.0000 3.0000 sum= 3.0000 Nv(i): 1.5000 1.5000 0.0000 sum= 3.0000 A(i): -0.0000 -0.0000 0.0130 B(i): 0.0016 0.0056 -0.0000 LWL85: dS = 0.0094 dN = 0.0027 w = 0.2903 S = 322.8 N = 1102.2 LWL85m: dS = 0.0060 dN = 0.0033 w = 0.5399 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0060 dN = 0.0025 w = 0.4178 7 (WHR1_DNA225) vs. 5 (Pmex37_DNA21) L(i): 923.0 269.5 232.5 sum= 1425.0 Ns(i): 1.5000 0.5000 2.0000 sum= 4.0000 Nv(i): 0.5000 1.5000 0.0000 sum= 2.0000 A(i): 0.0016 0.0019 0.0087 B(i): 0.0005 0.0056 -0.0000 LWL85: dS = 0.0078 dN = 0.0032 w = 0.4075 S = 322.3 N = 1102.7 LWL85m: dS = 0.0050 dN = 0.0038 w = 0.7582 S = 502.0 N = 923.0 (rho = 1.000) LPB93: dS = 0.0050 dN = 0.0033 w = 0.6602 7 (WHR1_DNA225) vs. 6 (Ptre197_DNA2) L(i): 923.0 269.5 232.5 sum= 1425.0 Ns(i): 4.0000 0.0000 4.0000 sum= 8.0000 Nv(i): 2.0000 1.0000 0.0000 sum= 3.0000 A(i): 0.0044 -0.0000 0.0175 B(i): 0.0022 0.0037 -0.0000 LWL85: dS = 0.0126 dN = 0.0064 w = 0.5052 S = 322.3 N = 1102.7 LWL85m: dS = 0.0081 dN = 0.0076 w = 0.9400 S = 502.0 N = 923.0 (rho = 1.000) LPB93: dS = 0.0081 dN = 0.0069 w = 0.8491 8 (YALD273_DNA5) vs. 1 (Pdel181_DNA2) L(i): 922.5 269.0 233.5 sum= 1425.0 Ns(i): 1.5000 0.5000 1.0000 sum= 3.0000 Nv(i): 1.0000 1.0000 0.0000 sum= 2.0000 A(i): 0.0016 0.0019 0.0043 B(i): 0.0011 0.0037 -0.0000 LWL85: dS = 0.0047 dN = 0.0032 w = 0.6832 S = 323.2 N = 1101.8 LWL85m: dS = 0.0030 dN = 0.0038 w = 1.2689 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0030 dN = 0.0033 w = 1.1052 8 (YALD273_DNA5) vs. 2 (Pfre186_DNA2) L(i): 922.5 269.5 233.0 sum= 1425.0 Ns(i): 2.5000 0.5000 1.0000 sum= 4.0000 Nv(i): 1.0000 1.0000 0.0000 sum= 2.0000 A(i): 0.0027 0.0019 0.0043 B(i): 0.0011 0.0037 -0.0000 LWL85: dS = 0.0047 dN = 0.0041 w = 0.8779 S = 322.8 N = 1102.2 LWL85m: dS = 0.0030 dN = 0.0049 w = 1.6325 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0030 dN = 0.0044 w = 1.4686 8 (YALD273_DNA5) vs. 3 (Pgra187_DNA2) L(i): 922.5 270.0 232.5 sum= 1425.0 Ns(i): 4.0000 1.0000 2.0000 sum= 7.0000 Nv(i): 1.5000 1.5000 0.0000 sum= 3.0000 A(i): 0.0044 0.0037 0.0087 B(i): 0.0016 0.0056 -0.0000 LWL85: dS = 0.0094 dN = 0.0064 w = 0.6803 S = 322.5 N = 1102.5 LWL85m: dS = 0.0060 dN = 0.0076 w = 1.2668 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0060 dN = 0.0069 w = 1.1440 8 (YALD273_DNA5) vs. 4 (Phet26_DNA21) L(i): 922.0 270.0 233.0 sum= 1425.0 Ns(i): 0.0000 0.0000 0.0000 sum= 0.0000 Nv(i): 0.0000 0.0000 0.0000 sum= 0.0000 A(i): 0.0000 0.0000 0.0000 B(i): -0.0000 -0.0000 -0.0000 LWL85: dS = 0.0000 dN = 0.0000 w = nan S = 323.0 N = 1102.0 LWL85m: dS = nan dN = nan w = nan S = nan N = nan (rho = nan) LPB93: dS = 0.0000 dN = 0.0000 w = nan 8 (YALD273_DNA5) vs. 5 (Pmex37_DNA21) L(i): 922.5 270.0 232.5 sum= 1425.0 Ns(i): 1.5000 0.5000 1.0000 sum= 3.0000 Nv(i): 1.0000 0.0000 0.0000 sum= 1.0000 A(i): 0.0016 0.0019 0.0043 B(i): 0.0011 -0.0000 -0.0000 LWL85: dS = 0.0047 dN = 0.0023 w = 0.4868 S = 322.5 N = 1102.5 LWL85m: dS = 0.0030 dN = 0.0027 w = 0.9065 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0030 dN = 0.0025 w = 0.8244 8 (YALD273_DNA5) vs. 6 (Ptre197_DNA2) L(i): 922.5 270.0 232.5 sum= 1425.0 Ns(i): 4.0000 0.0000 3.0000 sum= 7.0000 Nv(i): 1.5000 0.5000 0.0000 sum= 2.0000 A(i): 0.0044 -0.0000 0.0131 B(i): 0.0016 0.0019 -0.0000 LWL85: dS = 0.0094 dN = 0.0055 w = 0.5801 S = 322.5 N = 1102.5 LWL85m: dS = 0.0060 dN = 0.0065 w = 1.0802 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0060 dN = 0.0060 w = 0.9989 8 (YALD273_DNA5) vs. 7 (WHR1_DNA225) L(i): 922.5 269.5 233.0 sum= 1425.0 Ns(i): 0.0000 0.0000 3.0000 sum= 3.0000 Nv(i): 1.5000 1.5000 0.0000 sum= 3.0000 A(i): -0.0000 -0.0000 0.0130 B(i): 0.0016 0.0056 -0.0000 LWL85: dS = 0.0094 dN = 0.0027 w = 0.2903 S = 322.8 N = 1102.2 LWL85m: dS = 0.0060 dN = 0.0033 w = 0.5399 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0060 dN = 0.0025 w = 0.4178 9 (Pop_trich_ch) vs. 1 (Pdel181_DNA2) L(i): 922.5 269.0 233.5 sum= 1425.0 Ns(i): 1.5000 0.5000 1.0000 sum= 3.0000 Nv(i): 1.0000 1.0000 0.0000 sum= 2.0000 A(i): 0.0016 0.0019 0.0043 B(i): 0.0011 0.0037 -0.0000 LWL85: dS = 0.0047 dN = 0.0032 w = 0.6832 S = 323.2 N = 1101.8 LWL85m: dS = 0.0030 dN = 0.0038 w = 1.2689 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0030 dN = 0.0033 w = 1.1052 9 (Pop_trich_ch) vs. 2 (Pfre186_DNA2) L(i): 922.5 269.5 233.0 sum= 1425.0 Ns(i): 2.5000 0.5000 1.0000 sum= 4.0000 Nv(i): 1.0000 1.0000 0.0000 sum= 2.0000 A(i): 0.0027 0.0019 0.0043 B(i): 0.0011 0.0037 -0.0000 LWL85: dS = 0.0047 dN = 0.0041 w = 0.8779 S = 322.8 N = 1102.2 LWL85m: dS = 0.0030 dN = 0.0049 w = 1.6325 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0030 dN = 0.0044 w = 1.4686 9 (Pop_trich_ch) vs. 3 (Pgra187_DNA2) L(i): 922.5 270.0 232.5 sum= 1425.0 Ns(i): 4.0000 1.0000 2.0000 sum= 7.0000 Nv(i): 1.5000 1.5000 0.0000 sum= 3.0000 A(i): 0.0044 0.0037 0.0087 B(i): 0.0016 0.0056 -0.0000 LWL85: dS = 0.0094 dN = 0.0064 w = 0.6803 S = 322.5 N = 1102.5 LWL85m: dS = 0.0060 dN = 0.0076 w = 1.2668 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0060 dN = 0.0069 w = 1.1440 9 (Pop_trich_ch) vs. 4 (Phet26_DNA21) L(i): 922.0 270.0 233.0 sum= 1425.0 Ns(i): 0.0000 0.0000 0.0000 sum= 0.0000 Nv(i): 0.0000 0.0000 0.0000 sum= 0.0000 A(i): 0.0000 0.0000 0.0000 B(i): -0.0000 -0.0000 -0.0000 LWL85: dS = 0.0000 dN = 0.0000 w = nan S = 323.0 N = 1102.0 LWL85m: dS = nan dN = nan w = nan S = nan N = nan (rho = nan) LPB93: dS = 0.0000 dN = 0.0000 w = nan 9 (Pop_trich_ch) vs. 5 (Pmex37_DNA21) L(i): 922.5 270.0 232.5 sum= 1425.0 Ns(i): 1.5000 0.5000 1.0000 sum= 3.0000 Nv(i): 1.0000 0.0000 0.0000 sum= 1.0000 A(i): 0.0016 0.0019 0.0043 B(i): 0.0011 -0.0000 -0.0000 LWL85: dS = 0.0047 dN = 0.0023 w = 0.4868 S = 322.5 N = 1102.5 LWL85m: dS = 0.0030 dN = 0.0027 w = 0.9065 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0030 dN = 0.0025 w = 0.8244 9 (Pop_trich_ch) vs. 6 (Ptre197_DNA2) L(i): 922.5 270.0 232.5 sum= 1425.0 Ns(i): 4.0000 0.0000 3.0000 sum= 7.0000 Nv(i): 1.5000 0.5000 0.0000 sum= 2.0000 A(i): 0.0044 -0.0000 0.0131 B(i): 0.0016 0.0019 -0.0000 LWL85: dS = 0.0094 dN = 0.0055 w = 0.5801 S = 322.5 N = 1102.5 LWL85m: dS = 0.0060 dN = 0.0065 w = 1.0802 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0060 dN = 0.0060 w = 0.9989 9 (Pop_trich_ch) vs. 7 (WHR1_DNA225) L(i): 922.5 269.5 233.0 sum= 1425.0 Ns(i): 0.0000 0.0000 3.0000 sum= 3.0000 Nv(i): 1.5000 1.5000 0.0000 sum= 3.0000 A(i): -0.0000 -0.0000 0.0130 B(i): 0.0016 0.0056 -0.0000 LWL85: dS = 0.0094 dN = 0.0027 w = 0.2903 S = 322.8 N = 1102.2 LWL85m: dS = 0.0060 dN = 0.0033 w = 0.5399 S = 502.5 N = 922.5 (rho = 1.000) LPB93: dS = 0.0060 dN = 0.0025 w = 0.4178 9 (Pop_trich_ch) vs. 8 (YALD273_DNA5) L(i): 922.0 270.0 233.0 sum= 1425.0 Ns(i): 0.0000 0.0000 0.0000 sum= 0.0000 Nv(i): 0.0000 0.0000 0.0000 sum= 0.0000 A(i): 0.0000 0.0000 0.0000 B(i): -0.0000 -0.0000 -0.0000 LWL85: dS = 0.0000 dN = 0.0000 w = nan S = 323.0 N = 1102.0 LWL85m: dS = nan dN = nan w = nan S = nan N = nan (rho = nan) LPB93: dS = 0.0000 dN = 0.0000 w = nan Bio-Tools-Phylo-PAML-1.7.3/t/data/cysprot.msf0000644000175000017500000001057413316145226021551 0ustar carandraugcarandraugPileUp MSF: 393 Type: P Check: 3400 .. Name: CATH_HUMAN oo Len: 393 Check: 4989 Weight: 10.0 Name: CATH_RAT oo Len: 393 Check: 6434 Weight: 10.6 Name: ALEU_HORVU oo Len: 393 Check: 5288 Weight: 16.7 Name: PAPA_CARPA oo Len: 393 Check: 3242 Weight: 18.9 Name: CATL_HUMAN oo Len: 393 Check: 4708 Weight: 12.2 Name: CATL_RAT oo Len: 393 Check: 6797 Weight: 12.2 Name: CYS1_DICDI oo Len: 393 Check: 1942 Weight: 18.9 // CATH_HUMAN ....MWATLP LLCAGAWLLG VPVCGAAELS VN........ .......... CATH_RAT ....MWTALP LLCAGAWLLS AGAT..AELT VN........ .......... ALEU_HORVU ....MAHARV LLLALAVLAT AAVAVASSSS FADSNPIRPV TDRAASTLES PAPA_CARPA MAMIPSISKL LFVAICLFVY MGLSFGDFSI VG........ .........Y CATL_HUMAN ......MNPT LILAAFCLGI ASATLTFDHS LE........ .......... CATL_RAT ......MTPL LLLAVLCLGT ALATPKFDQT FN........ .......... CYS1_DICDI ......MKVI LLFVLAVFTV FVSSRGIPPE EQ........ .......... CATH_HUMAN ........SL EKFHFKSWMS KHRKTYS.TE EYHHRLQTFA SNWRKINAHN CATH_RAT ........AI EKFHFTSWMK QHQKTYS.SR EYSHRLQVFA NNWRKIQAHN ALEU_HORVU AVLGALGRTR HALRFARFAV RYGKSYESAA EVRRRFRIFS ESLEEVRSTN PAPA_CARPA SQNDLTSTER LIQLFESWML KHNKIYKNID EKIYRFEIFK DNLKYIDETN CATL_HUMAN .......... ..AQWTKWKA MHNRLYG.MN EEGWRRAVWE KNMKMIELHN CATL_RAT .......... ..AQWHQWKS THRRLYG.TN EEEWRRAVWE KNMRMIQLHN CYS1_DICDI .......... ..SQFLEFQD KFNKKYS.HE EYLERFEIFK SNLGKIEELN CATH_HUMAN ....NGNHTF KMALNQFSDM SFAEIKHKYL WSEPQNCSAT KS..NYLRGT CATH_RAT ....QRNHTF KMGLNQFSDM SFAEIKHKYL WSEPQNCSAT KS..NYLRGT ALEU_HORVU ....RKGLPY RLGINRFSDM SWEEFQATRL G.AAQTCSAT LAGNHLMRDA PAPA_CARPA ....KKNNSY WLGLNVFADM SNDEFKEKYT GSIAGNYTTT ELSYEEVLND CATL_HUMAN QEYREGKHSF TMAMNAFGDM TSEEFRQVMN GFQ....NRK PRKGKVFQEP CATL_RAT GEYSNGKHGF TMEMNAFGDM TNEEFRQIVN GYR....HQK HKKGRLFQEP CYS1_DICDI LIAINHKADT KFGVNKFADL SSDEFKNYYL NNKEAIFTDD LPVADYLDDE CATH_HUMAN G..PYPPSVD WRKKGNFVSP VKNQGACGSC WTFSTTGALE SAIAIATGKM CATH_RAT G..PYPSSMD WRKKGNVVSP VKNQGACGSC WTFSTTGALE SAVAIASGKM ALEU_HORVU A..ALPETKD WREDG.IVSP VKNQAHCGSC WTFSTTGALE AAYTQATGKN PAPA_CARPA GDVNIPEYVD WRQKG.AVTP VKNQGSCGSC WAFSAVVTIE GIIKIRTGNL CATL_HUMAN LFYEAPRSVD WREKG.YVTP VKNQGQCGSC WAFSATGALE GQMFRKTGRL CATL_RAT LMLQIPKTVD WREKG.CVTP VKNQGQCGSC WAFSASGCLE GQMFLKTGKL CYS1_DICDI FINSIPTAFD WRTRG.AVTP VKNQGQCGSC WSFSTTGNVE GQHFISQNKL CATH_HUMAN LSLAEQQLVD CAQDF..... ...NNYGCQG GLPSQAFEYI LYNKGIMGED CATH_RAT MTLAEQQLVD CAQNF..... ...NNHGCQG GLPSQAFEYI LYNKGIMGED ALEU_HORVU ISLSEQQLVD CAGGF..... ...NNFGCNG GLPSQAFEYI KYNGGIDTEE PAPA_CARPA NEYSEQELLD CDR....... ...RSYGCNG GYPWSALQLV AQYG.IHYRN CATL_HUMAN ISLSEQNLVD CSGP....QG ....NEGCNG GLMDYAFQYV QDNGGLDSEE CATL_RAT ISLSEQNLVD CSHD....QG ....NQGCNG GLMDFAFQYI KENGGLDSEE CYS1_DICDI VSLSEQNLVD CDHECMEYEG EEACDEGCNG GLQPNAYNYI IKNGGIQTES CATH_HUMAN TYPYQGKDGY .CKFQPGKAI GFVKDVANIT IYDEEAMVEA VALYNPVSFA CATH_RAT SYPYIGKNGQ .CKFNPEKAV AFVKNVVNIT LNDEAAMVEA VALYNPVSFA ALEU_HORVU SYPYKGVNGV .CHYKAENAA VQVLDSVNIT LNAEDELKNA VGLVRPVSVA PAPA_CARPA TYPYEGVQRY .CRSREKGPY AAKTDGVRQV QPYNEGALLY SIANQPVSVV CATL_HUMAN SYPYEATEES .CKYNPKYSV ANDTGFVDIP K.QEKALMKA VATVGPISVA CATL_RAT SYPYEAKDGS .CKYRAEYAV ANDTGFVDIP Q.QEKALMKA VATVGPISVA CYS1_DICDI SYPYTAETGT QCNFNSANIG AKISNFTMIP K.NETVMAGY IVSTGPLAIA CATH_HUMAN FEVT.QDFMM YRTGIYSSTS CHKTPDKVNH AVLAVGYGEK NG.....IPY CATH_RAT FEVT.EDFMM YKSGVYSSNS CHKTPDKVNH AVLAVGYGEQ NG.....LLY ALEU_HORVU FQVI.DGFRQ YKSGVYTSDH CGTTPDDVNH AVLAVGYGVE NG.....VPY PAPA_CARPA LEAAGKDFQL YRGGIFVG.. ..PCGNKVDH AVAAVGYGPN .........Y CATL_HUMAN IDAGHESFLF YKEGIYFEPD ..CSSEDMDH GVLVVGYGFE STESDNNK.Y CATL_RAT MDASHPSLQF YSSGIYYEPN ..CSSKDLDH GVLVVGYGYE GTDSNKDK.Y CYS1_DICDI ADA..VEWQF YIGGVFDIP. ..CNPNSLDH GILIVGYSAK NTIFRKNMPY CATH_HUMAN WIVKNSWGPQ WGMNGYFLIE RGK....NMC GLAACASYPI PLV CATH_RAT WIVKNSWGSN WGNNGYFLIE RGK....NMC GLAACASYPI PQV ALEU_HORVU WLIKNSWGAD WGDNGYFKME MGK....NMC AIATCASYPV VAA PAPA_CARPA ILIKNSWGTG WGENGYIRIK RGTGNSYGVC GLYTSSFYPV KN. CATL_HUMAN WLVKNSWGEE WGMGGYVKMA KDRR...NHC GIASAASYPT V.. CATL_RAT WLVKNSWGKE WGMDGYIKIA KDRN...NHC GLATAASYPI VN. CYS1_DICDI WIVKNSWGAD WGEQGYIYLR RGK....NTC GVSNFVSTSI I.. Bio-Tools-Phylo-PAML-1.7.3/t/data/gf-s85.phylip0000644000175000017500000000441413316145226021573 0ustar carandraugcarandraug 2 1128 gf.s85.4 ATGGATGTGATTGAGGAACACACGTGTATCGATGTCAATGCCATCCTTAAGCAGTTTCATGATTGGACGGTACTTCTCGAAGTTCGGCTCGCTTACTCTTCTCTATACACCTTCATCTTTGTTACCGGAGTAATTGGAAATGGTCTTCTGATATCATCGATTCTGCTCAGAAAAAAGTTATCAGTTGCCAACATATTTCTTATCAATTTGGCAGTATCTGATTTGCTCCTATGCATCACCGCCGTACCGATCACTCCAGTGTTGGCGTTTATGAAACGATGGATGTTCGGAATATTCATGTGCAAATTGGTTCCCGCTTGTCAAGCATTTTCGGTGCTCATTTCATCCTGGTCTTTGTGCTACATTGCAATTGACCGATATAGAAGTATAGTGACGCCATTGAGGGAACCATGGTCCGATAGGCATGCGAGGTGGCTTCTGATATTCACTTGGGTCGTAGCATTCCTGGCCAGTTATCCACTTTACTACTCACAAAATTTGAAAACTATGGTTATCGAAAATGTTACTCTTTGTGGAGATTTCTGTGGTGAATTCAACTGGCAATCCGACGAGCTATCGAAACTAATCTATACAACAAGTTTACTCATTATTCAGCTGATAATTCCAGCCATTATCATGTCATTTTGCTATTGGAAAATCTTACAAAAGGTGCGTACGGACTGGCTGGTCGACGAAGGATCCATGCTTACTGCGGCGCAACAGGCTCAAACAGCAGTTCGAAAGCGACGAGTGATGTACGTGTTGATTCTGATGGTCATCGTATTCATGGCATGCTGGTTCCCATTATCCGTAGTCAAT---------------------------------TGTTCCGTGATCTCGGAA---------------------------------------------------------------------------------------------TGCGATTCGCGACATCGGCGAGCACTAAAAGACGACATGACGTGGCTAACCAACGCCCGTCGTCATACCAATGTAGGCGTTCTATCTCGCTTCACACCTTCTCCATCAGTCTCCGTAGTTTACCGACGAACTTTGGAGCGACATCTCGGCGTCAATCATTTCCGG ZC412.1 atgggtgatgctgaatctcatcattgtatagatgtgaacgccattcttcagcagttcaatgattggacagtcctctttgaagttcggcttggatattcagtactatactttctcatattaataatcggattggttggaaatgggctattgatcacttcaattttaatgcgaaagaaactttccgtggcaaacatattcttgataaacctggcagtttctgatttgcttctttgcatcacggcggtgccgatcactccagtattggcgtttatgaagcgatggatatttggaataattatgtgtaaattggttccaacttgtcaggcgttttcggtgctcatttcttcatggtctttgtgttacatcgcaattgatagatatcgaagtattgtgacgccactccgggaaccatggtctgataggcatgcaaggtggcttctgatgttcacatgggtggtcgccttccttgctagttatcctctatattactcacagaacttgaaaacaatggttattgaaaatgtgacattatgtggagatttttgcggcgagttcaattggcagtcggatgaaatatccaagttgacatatactacgagtttattgattattcagctgattattccagcaattatcatgtctttttgttatttaatgattctacaaaaggtacaaaccgactggcttgtcgacgagggatccatgttgactgccgcacaacaggctcaaacagcagttcgaaagcgacgagtgatgtacgtgttgattctaatggttattgtttttatggcttgctggttcccgttgtccgccgtgaatttgttcagagatctcggaatgcgattcgagttctgtcaaactgtttacaaggttttaatgatggaccaaatgtatttcaagttgctcaatgtgcacgtcatcgcgatgacttcgatcgtatggaatccggtgctctatttctggatgagcaagcgtcatcgacgagccctgaaagacgacatgacgtggctcaccaatgctcgccgtcatacaaacgtcggcgttctgtctcgcttcacaccttctccatcagtttcagtggtttacagacgaactctggagcgacatctaggtgtcaatcatttccgc Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml4.mlc0000644000175000017500000004735213316145226021367 0ustar carandraugcarandraug seed used = 480745521 5 855 human GTG CTG TCT CCT GCC GAC AAG ACC AAC GTC AAG GCC GCC TGG GGC AAG GTT GGC GCG CAC GCT GGC GAG TAT GGT GCG GAG GCC CTG GAG AGG ATG TTC CTG TCC TTC CCC ACC ACC AAG ACC TAC TTC CCG CAC TTC GAC CTG AGC CAC GGC TCT GCC CAG GTT AAG GGC CAC GGC AAG AAG GTG GCC GAC GCG CTG ACC AAC GCC GTG GCG CAC GTG GAC GAC ATG CCC AAC GCG CTG TCC GCC CTG AGC GAC CTG CAC GCG CAC AAG CTT CGG GTG GAC CCG GTC AAC TTC AAG CTC CTA AGC CAC TGC CTG CTG GTG ACC CTG GCC GCC CAC CTC CCC GCC GAG TTC ACC CCT GCG GTG CAC GCC TCC CTG GAC AAG TTC CTG GCT TCT GTG AGC ACC GTG CTG ACC TCC AAA TAC CGT CTG ACT CCT GAG GAG AAG TCT GCC GTT ACT GCC CTG TGG GGC AAG GTG AAC GTG GAT GAA GTT GGT GGT GAG GCC CTG GGC AGG CTG CTG GTG GTC TAC CCT TGG ACC CAG AGG TTC TTT GAG TCC TTT GGG GAT CTG TCC ACT CCT GAT GCT GTT ATG GGC AAC CCT AAG GTG AAG GCT CAT GGC AAG AAA GTG CTC GGT GCC TTT AGT GAT GGC CTG GCT CAC CTG GAC AAC CTC AAG GGC ACC TTT GCC ACA CTG AGT GAG CTG CAC TGT GAC AAG CTG CAC GTG GAT CCT GAG AAC TTC AGG CTC CTG GGC AAC GTG CTG GTC TGT GTG CTG GCC CAT CAC TTT GGC AAA GAA TTC ACC CCA CCA GTG CAG GCT GCC TAT CAG AAA GTG GTG GCT GGT GTG GCT AAT GCC CTG GCC CAC AAG TAT CAC goat-cow GTG CTG TCT GCC GCC GAC AAG TCC AAT GTC AAG GCC GCC TGG GGC AAG GTT GGC GGC AAC GCT GGA GCT TAT GGC GCA GAG GCT CTG GAG AGG ATG TTC CTG AGC TTC CCC ACC ACC AAG ACC TAC TTC CCC CAC TTC GAC CTG AGC CAC GGC TCG GCC CAG GTC AAG GGC CAC GGC GAG AAG GTG GCC GCC GCG CTG ACC AAA GCG GTG GGC CAC CTG GAC GAC CTG CCC GGT ACT CTG TCT GAT CTG AGT GAC CTG CAC GCC CAC AAG CTG CGT GTG GAC CCG GTC AAC TTT AAG CTT CTG AGC CAC TCC CTG CTG GTG ACC CTG GCC TGC CAC CTC CCC AAT GAT TTC ACC CCC GCG GTC CAC GCC TCC CTG GAC AAG TTC TTG GCC AAC GTG AGC ACC GTG CTG ACC TCC AAA TAC CGT CTG ACT GCT GAG GAG AAG GCT GCC GTC ACC GCC TTT TGG GGC AAG GTG AAA GTG GAT GAA GTT GGT GGT GAG GCC CTG GGC AGG CTG CTG GTT GTC TAC CCC TGG ACT CAG AGG TTC TTT GAG TCC TTT GGG GAC TTG TCC ACT GCT GAT GCT GTT ATG AAC AAC CCT AAG GTG AAG GCC CAT GGC AAG AAG GTG CTA GAT TCC TTT AGT AAT GGC ATG AAG CAT CTC GAT GAC CTC AAG GGC ACC TTT GCT GCG CTG AGT GAG CTG CAC TGT GAT AAG CTG CAT GTG GAT CCT GAG AAC TTC AAG CTC CTG GGC AAC GTG CTA GTG GTT GTG CTG GCT CGC AAT TTT GGC AAG GAA TTC ACC CCG GTG CTG CAG GCT GAC TTT CAG AAG GTG GTG GCT GGT GTG GCC AAT GCC CTG GCC CAC AGA TAT CAT rabbit GTG CTG TCT CCC GCT GAC AAG ACC AAC ATC AAG ACT GCC TGG GAA AAG ATC GGC AGC CAC GGT GGC GAG TAT GGC GCC GAG GCC GTG GAG AGG ATG TTC TTG GGC TTC CCC ACC ACC AAG ACC TAC TTC CCC CAC TTC GAC TTC ACC CAC GGC TCT GAG CAG ATC AAA GCC CAC GGC AAG AAG GTG TCC GAA GCC CTG ACC AAG GCC GTG GGC CAC CTG GAC GAC CTG CCC GGC GCC CTG TCT ACT CTC AGC GAC CTG CAC GCG CAC AAG CTG CGG GTG GAC CCG GTG AAT TTC AAG CTC CTG TCC CAC TGC CTG CTG GTG ACC CTG GCC AAC CAC CAC CCC AGT GAA TTC ACC CCT GCG GTG CAT GCC TCC CTG GAC AAG TTC CTG GCC AAC GTG AGC ACC GTG CTG ACC TCC AAA TAT CGT CTG TCC AGT GAG GAG AAG TCT GCG GTC ACT GCC CTG TGG GGC AAG GTG AAT GTG GAA GAA GTT GGT GGT GAG GCC CTG GGC AGG CTG CTG GTT GTC TAC CCA TGG ACC CAG AGG TTC TTC GAG TCC TTT GGG GAC CTG TCC TCT GCA AAT GCT GTT ATG AAC AAT CCT AAG GTG AAG GCT CAT GGC AAG AAG GTG CTG GCT GCC TTC AGT GAG GGT CTG AGT CAC CTG GAC AAC CTC AAA GGC ACC TTT GCT AAG CTG AGT GAA CTG CAC TGT GAC AAG CTG CAC GTG GAT CCT GAG AAC TTC AGG CTC CTG GGC AAC GTG CTG GTT ATT GTG CTG TCT CAT CAT TTT GGC AAA GAA TTC ACT CCT CAG GTG CAG GCT GCC TAT CAG AAG GTG GTG GCT GGT GTG GCC AAT GCC CTG GCT CAC AAA TAC CAC rat GTG CTC TCT GCA GAT GAC AAA ACC AAC ATC AAG AAC TGC TGG GGG AAG ATT GGT GGC CAT GGT GGT GAA TAT GGC GAG GAG GCC CTA CAG AGG ATG TTC GCT GCC TTC CCC ACC ACC AAG ACC TAC TTC TCT CAC ATT GAT GTA AGC CCC GGC TCT GCC CAG GTC AAG GCT CAC GGC AAG AAG GTT GCT GAT GCC TTG GCC AAA GCT GCA GAC CAC GTC GAA GAC CTG CCT GGT GCC CTG TCC ACT CTG AGC GAC CTG CAT GCC CAC AAA CTG CGT GTG GAT CCT GTC AAC TTC AAG TTC CTG AGC CAC TGC CTG CTG GTG ACC TTG GCT TGC CAC CAC CCT GGA GAT TTC ACA CCC GCC ATG CAC GCC TCT CTG GAC AAA TTC CTT GCC TCT GTG AGC ACT GTG CTG ACC TCC AAG TAC CGT CTA ACT GAT GCT GAG AAG GCT GCT GTT AAT GCC CTG TGG GGA AAG GTG AAC CCT GAT GAT GTT GGT GGC GAG GCC CTG GGC AGG CTG CTG GTT GTC TAC CCT TGG ACC CAG AGG TAC TTT GAT AGC TTT GGG GAC CTG TCC TCT GCC TCT GCT ATC ATG GGT AAC CCT AAG GTG AAG GCC CAT GGC AAG AAG GTG ATA AAC GCC TTC AAT GAT GGC CTG AAA CAC TTG GAC AAC CTC AAG GGC ACC TTT GCT CAT CTG AGT GAA CTC CAC TGT GAC AAG CTG CAT GTG GAT CCT GAG AAC TTC AGG CTC CTG GGC AAT ATG ATT GTG ATT GTG TTG GGC CAC CAC CTG GGC AAG GAA TTC ACC CCC TGT GCA CAG GCT GCC TTC CAG AAG GTG GTG GCT GGA GTG GCC AGT GCC CTG GCT CAC AAG TAC CAC marsupial GTG CTC TCG GAT GCT GAC AAG ACT CAC GTG AAA GCC ATC TGG GGT AAG GTG GGA GGC CAC GCC GGT GCC TAC GCA GCT GAA GCT CTT GCC AGA ACC TTC CTC TCC TTC CCC ACT ACC AAA ACT TAC TTC CCC CAC TTC GAC CTG TCC CCC GGC TCC GCC CAG ATC CAG GGT CAT GGT AAG AAG GTA GCC GAT GCC CTT TCC CAG GCT GTT GCC CAC CTG GAC GAC CTG CCC GGA ACC ATG TCC AAA CTA AGC GAC CTG CAC GCC CAC AAG CTG AGA GTG GAT CCC GTG AAC TTC AAG CTC CTC TCT CAC TGC CTG ATC GTG ACT CTG GCC GCC CAT CTG AGC AAG GAT TTG ACT CCC GAA GTG CAC GCC TCC ATG GAC AAG TTC TTT GCC TCT GTG GCT ACC GTG CTG ACC TCG AAG TAC CGT TTG ACT TCT GAG GAG AAG AAC TGC ATC ACT ACC ATC TGG TCT AAG GTG CAG GTT GAC CAG ACT GGT GGT GAG GCC CTT GGC AGG ATG CTC GTT GTC TAC CCC TGG ACC ACC AGG TTT TTT GGG AGC TTT GGT GAT CTG TCC TCT CCT GGC GCT GTC ATG TCA AAT TCT AAG GTT CAA GCC CAT GGT GCT AAG GTG TTG ACC TCC TTC GGT GAA GCA GTC AAG CAT TTG GAC AAC CTG AAG GGT ACT TAT GCC AAG TTG AGT GAG CTC CAC TGT GAC AAG CTG CAT GTG GAC CCT GAG AAC TTC AAG ATG CTG GGG AAT ATC ATT GTG ATC TGC CTG GCT GAG CAC TTT GGC AAG GAT TTT ACT CCT GAA TGT CAG GTT GCT TGG CAG AAG CTC GTG GCT GGA GTT GCC CAT GCC CTG GCC CAC AAG TAC CAC Printing out site pattern counts 5 669 P human GTG CTG TCT CCT GCC GAC AAG ACC AAC GTC AAG GCC GCC TGG GGC AAG GTT GGC GCG CAC GCT GGC GAG TAT GGT GCG GAG GCC CTG GAG AGG ATG TTC CTG TCC CCC ACC ACC TAC CCG CAC TTC GAC CTG AGC CAC GGC TCT GCC CAG GTT AAG GGC CAC GGC AAG GTG GCC GAC GCG CTG ACC AAC GCC GTG GCG GTG GAC ATG CCC AAC GCG CTG TCC GCC CTG AGC CTG CAC GCG CTT CGG GAC CCG GTC AAC TTC CTC CTA AGC TGC CTG CTG GCC GCC CTC CCC GCC GAG TTC ACC CCT GCG GTG CAC GCC TCC CTG GCT TCT AGC ACC TCC AAA TAC CGT CTG ACT CCT GAG GAG TCT GCC GTT ACT GCC CTG GGC AAC GTG GAT GAA GTT GGT GGT CTG AGG CTG GTG GTC CCT ACC CAG TTC TTT GAG TCC TTT GGG GAT CTG TCC ACT CCT GAT GCT GTT ATG GGC AAC CCT GTG AAG GCT CAT AAG AAA CTC GGT GCC TTT AGT GAT GGC CTG GCT CAC CTG GAC AAC CTC AAG TTT GCC ACA CTG AGT GAG TGT CAC GAT CCT AAC AGG CTC GGC AAC GTG CTG GTC TGT GTG GCC CAT CAC TTT AAA GAA TTC ACC CCA CCA GTG GCT GCC TAT GTG GGT AAT GCC AAG TAT CAC goat-cow ... ... ... G.C ... ... ... T.. ..T ... ... ... ... ... ... ... ... ... .GC A.. ... ..A .CT ... ..C ..A ... ..T ... ... ... ... ... ... AG. ... ... ... ... ..C ... ... ... ... ... ... ... ..G ... ... ..C ... ... ... ... G.. ... ... .C. ... ... ... ..A ..G ... .GC C.. ... C.. ... GGT A.T ... ..T .AT ... ..T ... ... ..C ..G ..T ... ... ... ... ..T ..T ..G ... .C. ... ... ... TG. ... ... AAT ..T ... ... ..C ... ..C ... ... ... T.. ..C AAC ... ... ... ... ... ... ... ... G.. ... ... G.. ... ..C ..C ... T.T ... ..A ... ... ... ... ... ... ... ... ... ..T ... ..C ..T ... ... ... ... ... ... ... ..C T.. ... ... G.. ... ... ... ... AA. ... ... ... ... ..C ... ... ..G ..A .A. T.. ... ... A.. ... A.. AAG ..T ..C ..T G.. ... ... ... ..T G.G ... ... ... ... ..T ... ... ... .A. ... ... ... ... ..A ..G GT. ... ..T .GC A.T ... ..G ... ... ... ..G GTG C.. ... .A. .T. ... ... ... ... .GA ... ..T rabbit ... ... ... ..C ..T ... ... ... ... A.. ... A.T ... ... .AA ... A.C ... AGC ... .G. ... ... ... ..C ..C ... ... G.. ... ... ... ... T.. GG. ... ... ... ... ..C ... ... ... T.C .C. ... ... ... .AG ... A.C ..A .C. ... ... ... ... T.. ..A ..C ... ... ..G ... ... .GC C.. ... C.. ... GG. ..C ... ..T A.T ..C ... ... ... ... ..G ... ... ... ..G ..T ... ... ..G TC. ... ... ... ... AA. .A. ... AGT ..A ... ... ... ... ... ..T ... ... ... ..C AAC ... ... ... ... ..T ... ... T.C AG. ... ... ... ..G ..C ... ... ... ... ..T ... ..A ... ... ... ... ... ... ... ..T ... ..A ... ... ... ..C ... ... ... ... ..C ... ... T.. G.A A.. ... ... ... AA. ..T ... ... ... ... ... ... ..G ..G .C. ... ..C ... ..G ..T ... AG. ... ... ... ... ... ..A ... ..T .AG ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ..T AT. ... T.T ... ..T ... ... ... ... ..T ..T .AG ... ... ... ... ... ... ... ..T ..A ..C ... rat ... ..C ... G.A .AT ... ..A ... ... A.. ... AA. TG. ... ..G ... A.. ..T .GC ..T .G. ..T ..A ... ..C .A. ... ... ..A C.. ... ... ... GCT G.. ... ... ... ... T.T ... A.T ..T G.A ... .C. ... ... ... ... ..C ... .CT ... ... ... ..T ..T ..T ..C T.. G.. ..A ..T .CA .AC ..C ..A C.. ..T GGT ..C ... ... A.T ... ... ... ..T ..C ..G ..T ..T ..T ... ... ... T.. ..G ... ... ... T.. ..T TG. .A. ..T .GA ..T ... ..A ..C ..C A.. ... ... ..T ..T ..C ... ... ..T ... ..G ... ... ..A ... GA. .CT ... G.. ..T ... .A. ... ... ..A ... CCT ... ..T ... ... ..C ... ... ... ..T ... ... ... ... .A. ... ..T AG. ... ... ..C ... ... T.. G.C TC. ... A.C ... ..T ... ... ... ... ..C ... ... ..G A.A AAC ... ..C .A. ... ... ... AAA ... T.. ... ... ... ... ... ..T CAT ... ... ..A ... ..T ... ... ... ... ... ... ..T A.. A.T ..G AT. ... .G. ..C ... C.G ..G ... ... ... ..C TGT .CA ... ... .TC ... ..A .G. ..T ... ..C ... marsupial ... ..C ..G GA. ..T ... ... ..T C.. ..G ..A ... AT. ... ..T ... ..G ..A .GC ... ..C ..T .CC ..C .CA ..T ..A ..T ..T .CC ..A .CC ... ..C ... ... ..T ... ... ..C ... ... ... ... TC. .C. ... ..C ... ... A.C C.. ..T ..T ..T ... ..A ... ..T ..C ..T T.. C.G ..T ..T ..C C.. ... C.. ... GGA A.C A.. ... AAA ..A ... ... ... ..C ..G A.A ..T ..C ..G ... ... ... ..C TCT ... A.C ... ... ... ..G AG. AAG ..T ..G ..T ..C .AA ... ... ... ... T.T ..C ... GCT ... ..G ..G ... ... T.. ... T.. ... ... AAC TG. A.C ... A.. A.C TCT C.G ..T ..C C.G AC. ... ... ..T ... ..C ..T ... ..C ... ACC ..T ... .G. AG. ... ..T ... ... ... T.. ... .GC ... ..C ... TCA ..T T.. ..T C.A ..C ... GCT ..G T.G ACC T.. ..C G.. ..A .CA G.C AAG ..T T.. ... ... ..G ... .A. ... .AG T.. ... ... ... ..T ..C ... ... .A. A.G ..G ..T A.C A.T ..G ATC TGC ..T G.G ... ... ..G ..T ..T ..T ..T GA. TGT .T. ..T .GG C.C ..A C.. ... ... ..C ... 9 2 1 1 1 4 3 1 1 1 2 1 1 3 1 7 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 5 1 1 1 4 2 2 1 6 1 1 1 1 1 3 1 1 3 1 1 1 2 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 1 6 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 2 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 2 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 CODONML (in paml version 4, June 2007) abglobin.nuc Model: One dN/dS ratio Codon frequencies: Fequal ns = 5 ls = 285 Codon usage in sequences -------------------------------------------------------------------------------------------------- Phe TTT 5 8 3 3 6 | Ser TCT 4 2 6 7 6 | Tyr TAT 3 2 3 1 1 | Cys TGT 2 1 1 2 2 TTC 10 9 13 11 8 | TCC 6 7 7 3 8 | TAC 3 3 3 5 5 | TGC 1 1 1 3 3 Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 TTG 0 2 1 4 5 | TCG 0 1 0 0 2 | TAG 0 0 0 0 0 | Trp TGG 3 3 3 3 4 -------------------------------------------------------------------------------------------------- Leu CTT 1 1 0 1 3 | Pro CCT 7 2 4 7 3 | His CAT 2 4 4 5 6 | Arg CGT 1 2 1 2 1 CTC 5 4 4 4 7 | CCC 3 6 5 4 7 | CAC 16 11 15 14 12 | CGC 0 1 0 0 0 CTA 1 2 0 2 1 | CCA 2 0 1 0 0 | Gln CAA 0 0 0 0 1 | CGA 0 0 0 0 0 CTG 29 28 30 21 15 | CCG 2 2 1 0 0 | CAG 4 4 5 5 7 | CGG 1 0 1 0 0 -------------------------------------------------------------------------------------------------- Ile ATT 0 0 1 4 1 | Thr ACT 3 4 4 3 10 | Asn AAT 1 5 5 3 2 | Ser AGT 2 3 5 2 1 ATC 0 0 3 2 7 | ACC 12 11 12 9 9 | AAC 9 7 7 8 4 | AGC 4 4 3 5 3 ATA 0 0 0 1 0 | ACA 1 0 0 1 0 | Lys AAA 4 3 5 5 3 | Arg AGA 0 1 0 0 2 Met ATG 3 3 2 4 5 | ACG 0 0 0 0 0 | AAG 18 21 19 19 21 | AGG 4 3 4 4 2 -------------------------------------------------------------------------------------------------- Val GTT 5 5 4 4 6 | Ala GCT 8 11 8 13 10 | Asp GAT 5 8 1 11 6 | Gly GGT 5 4 5 6 10 GTC 4 6 2 4 3 | GCC 21 18 16 18 19 | GAC 10 10 10 8 10 | GGC 14 15 14 12 5 GTA 0 0 0 1 1 | GCA 0 1 1 3 2 | Glu GAA 2 2 7 4 4 | GGA 0 1 0 3 3 GTG 21 19 21 14 14 | GCG 7 4 3 0 0 | GAG 10 9 10 5 6 | GGG 1 1 1 2 2 -------------------------------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: human position 1: T:0.12982 C:0.25965 A:0.21404 G:0.39649 position 2: T:0.29474 C:0.26667 A:0.30526 G:0.13333 position 3: T:0.18947 C:0.41404 A:0.03509 G:0.36140 Average T:0.20468 C:0.31345 A:0.18480 G:0.29708 #2: goat-cow position 1: T:0.13684 C:0.23509 A:0.22807 G:0.40000 position 2: T:0.30526 C:0.24211 A:0.31228 G:0.14035 position 3: T:0.21754 C:0.39649 A:0.03509 G:0.35088 Average T:0.21988 C:0.29123 A:0.19181 G:0.29708 #3: rabbit position 1: T:0.14386 C:0.24912 A:0.24561 G:0.36140 position 2: T:0.29474 C:0.23860 A:0.32982 G:0.13684 position 3: T:0.19298 C:0.40351 A:0.04912 G:0.35439 Average T:0.21053 C:0.29708 A:0.20819 G:0.28421 #4: rat position 1: T:0.14737 C:0.22807 A:0.24561 G:0.37895 position 2: T:0.28070 C:0.23860 A:0.32632 G:0.15439 position 3: T:0.25965 C:0.38596 A:0.07018 G:0.28421 Average T:0.22924 C:0.28421 A:0.21404 G:0.27251 #5: marsupial position 1: T:0.17895 C:0.22105 A:0.24561 G:0.35439 position 2: T:0.28772 C:0.27018 A:0.30877 G:0.13333 position 3: T:0.25965 C:0.38596 A:0.06316 G:0.29123 Average T:0.24211 C:0.29240 A:0.20585 G:0.25965 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 25 | Ser S TCT 25 | Tyr Y TAT 10 | Cys C TGT 8 TTC 51 | TCC 31 | TAC 19 | TGC 9 Leu L TTA 0 | TCA 1 | *** * TAA 0 | *** * TGA 0 TTG 12 | TCG 3 | TAG 0 | Trp W TGG 16 ------------------------------------------------------------------------------ Leu L CTT 6 | Pro P CCT 23 | His H CAT 21 | Arg R CGT 7 CTC 24 | CCC 25 | CAC 68 | CGC 1 CTA 6 | CCA 3 | Gln Q CAA 1 | CGA 0 CTG 123 | CCG 5 | CAG 25 | CGG 2 ------------------------------------------------------------------------------ Ile I ATT 6 | Thr T ACT 24 | Asn N AAT 16 | Ser S AGT 13 ATC 12 | ACC 53 | AAC 35 | AGC 19 ATA 1 | ACA 2 | Lys K AAA 20 | Arg R AGA 3 Met M ATG 17 | ACG 0 | AAG 98 | AGG 17 ------------------------------------------------------------------------------ Val V GTT 24 | Ala A GCT 50 | Asp D GAT 31 | Gly G GGT 30 GTC 19 | GCC 92 | GAC 48 | GGC 60 GTA 2 | GCA 7 | Glu E GAA 19 | GGA 7 GTG 89 | GCG 14 | GAG 40 | GGG 7 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.14737 C:0.23860 A:0.23579 G:0.37825 position 2: T:0.29263 C:0.25123 A:0.31649 G:0.13965 position 3: T:0.22386 C:0.39719 A:0.05053 G:0.32842 Average T:0.22129 C:0.29567 A:0.20094 G:0.28211 Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.00000000 0.00000000 0.01639344 0.01639344 0.00000000 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 0.01639344 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) human goat-cow 0.2507 (0.0863 0.3443) rabbit 0.2627 (0.0867 0.3301) 0.2943 (0.1054 0.3581) rat 0.2045 (0.1261 0.6164) 0.2462 (0.1493 0.6065) 0.2178 (0.1348 0.6187) marsupial 0.1902 (0.1931 1.0148) 0.1891 (0.1910 1.0099) 0.2184 (0.2111 0.9668) 0.2716 (0.2404 0.8852) pairwise comparison, codon frequencies: Fequal. 2 (goat-cow) ... 1 (human) lnL =-1596.739984 0.43894 1.87997 0.29075 t= 0.4389 S= 236.2 N= 618.8 dN/dS= 0.2908 dN= 0.0874 dS= 0.3006 3 (rabbit) ... 1 (human) lnL =-1593.524138 0.43016 1.74883 0.29827 t= 0.4302 S= 234.0 N= 621.0 dN/dS= 0.2983 dN= 0.0872 dS= 0.2924 3 (rabbit) ... 2 (goat-cow) lnL =-1634.706680 0.49216 1.87718 0.33712 t= 0.4922 S= 236.1 N= 618.9 dN/dS= 0.3371 dN= 0.1063 dS= 0.3154 4 (rat) ... 1 (human) lnL =-1722.645692 0.71450 1.56250 0.22967 t= 0.7145 S= 230.6 N= 624.4 dN/dS= 0.2297 dN= 0.1250 dS= 0.5445 4 (rat) ... 2 (goat-cow) lnL =-1750.493581 0.75917 2.15224 0.28700 t= 0.7592 S= 240.3 N= 614.7 dN/dS= 0.2870 dN= 0.1490 dS= 0.5192 4 (rat) ... 3 (rabbit) lnL =-1730.718528 0.73744 1.94983 0.24972 t= 0.7374 S= 237.3 N= 617.7 dN/dS= 0.2497 dN= 0.1340 dS= 0.5368 5 (marsupial) ... 1 (human) lnL =-1854.925323 1.18627 1.01786 0.17389 t= 1.1863 S= 218.3 N= 636.7 dN/dS= 0.1739 dN= 0.1787 dS= 1.0276 5 (marsupial) ... 2 (goat-cow) lnL =-1853.486254 1.12573 1.26005 0.19796 t= 1.1257 S= 224.3 N= 630.7 dN/dS= 0.1980 dN= 0.1819 dS= 0.9189 5 (marsupial) ... 3 (rabbit) lnL =-1873.309372 1.18527 1.16455 0.20554 t= 1.1853 S= 222.0 N= 633.0 dN/dS= 0.2055 dN= 0.1972 dS= 0.9593 5 (marsupial) ... 4 (rat) lnL =-1901.596050 1.20106 1.12357 0.24932 t= 1.2011 S= 221.0 N= 634.0 dN/dS= 0.2493 dN= 0.2251 dS= 0.9030 Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml43.mlc0000644000175000017500000004745013316145226021451 0ustar carandraugcarandraug seed used = 738594397 5 855 human GTG CTG TCT CCT GCC GAC AAG ACC AAC GTC AAG GCC GCC TGG GGC AAG GTT GGC GCG CAC GCT GGC GAG TAT GGT GCG GAG GCC CTG GAG AGG ATG TTC CTG TCC TTC CCC ACC ACC AAG ACC TAC TTC CCG CAC TTC GAC CTG AGC CAC GGC TCT GCC CAG GTT AAG GGC CAC GGC AAG AAG GTG GCC GAC GCG CTG ACC AAC GCC GTG GCG CAC GTG GAC GAC ATG CCC AAC GCG CTG TCC GCC CTG AGC GAC CTG CAC GCG CAC AAG CTT CGG GTG GAC CCG GTC AAC TTC AAG CTC CTA AGC CAC TGC CTG CTG GTG ACC CTG GCC GCC CAC CTC CCC GCC GAG TTC ACC CCT GCG GTG CAC GCC TCC CTG GAC AAG TTC CTG GCT TCT GTG AGC ACC GTG CTG ACC TCC AAA TAC CGT CTG ACT CCT GAG GAG AAG TCT GCC GTT ACT GCC CTG TGG GGC AAG GTG AAC GTG GAT GAA GTT GGT GGT GAG GCC CTG GGC AGG CTG CTG GTG GTC TAC CCT TGG ACC CAG AGG TTC TTT GAG TCC TTT GGG GAT CTG TCC ACT CCT GAT GCT GTT ATG GGC AAC CCT AAG GTG AAG GCT CAT GGC AAG AAA GTG CTC GGT GCC TTT AGT GAT GGC CTG GCT CAC CTG GAC AAC CTC AAG GGC ACC TTT GCC ACA CTG AGT GAG CTG CAC TGT GAC AAG CTG CAC GTG GAT CCT GAG AAC TTC AGG CTC CTG GGC AAC GTG CTG GTC TGT GTG CTG GCC CAT CAC TTT GGC AAA GAA TTC ACC CCA CCA GTG CAG GCT GCC TAT CAG AAA GTG GTG GCT GGT GTG GCT AAT GCC CTG GCC CAC AAG TAT CAC goat-cow GTG CTG TCT GCC GCC GAC AAG TCC AAT GTC AAG GCC GCC TGG GGC AAG GTT GGC GGC AAC GCT GGA GCT TAT GGC GCA GAG GCT CTG GAG AGG ATG TTC CTG AGC TTC CCC ACC ACC AAG ACC TAC TTC CCC CAC TTC GAC CTG AGC CAC GGC TCG GCC CAG GTC AAG GGC CAC GGC GAG AAG GTG GCC GCC GCG CTG ACC AAA GCG GTG GGC CAC CTG GAC GAC CTG CCC GGT ACT CTG TCT GAT CTG AGT GAC CTG CAC GCC CAC AAG CTG CGT GTG GAC CCG GTC AAC TTT AAG CTT CTG AGC CAC TCC CTG CTG GTG ACC CTG GCC TGC CAC CTC CCC AAT GAT TTC ACC CCC GCG GTC CAC GCC TCC CTG GAC AAG TTC TTG GCC AAC GTG AGC ACC GTG CTG ACC TCC AAA TAC CGT CTG ACT GCT GAG GAG AAG GCT GCC GTC ACC GCC TTT TGG GGC AAG GTG AAA GTG GAT GAA GTT GGT GGT GAG GCC CTG GGC AGG CTG CTG GTT GTC TAC CCC TGG ACT CAG AGG TTC TTT GAG TCC TTT GGG GAC TTG TCC ACT GCT GAT GCT GTT ATG AAC AAC CCT AAG GTG AAG GCC CAT GGC AAG AAG GTG CTA GAT TCC TTT AGT AAT GGC ATG AAG CAT CTC GAT GAC CTC AAG GGC ACC TTT GCT GCG CTG AGT GAG CTG CAC TGT GAT AAG CTG CAT GTG GAT CCT GAG AAC TTC AAG CTC CTG GGC AAC GTG CTA GTG GTT GTG CTG GCT CGC AAT TTT GGC AAG GAA TTC ACC CCG GTG CTG CAG GCT GAC TTT CAG AAG GTG GTG GCT GGT GTG GCC AAT GCC CTG GCC CAC AGA TAT CAT rabbit GTG CTG TCT CCC GCT GAC AAG ACC AAC ATC AAG ACT GCC TGG GAA AAG ATC GGC AGC CAC GGT GGC GAG TAT GGC GCC GAG GCC GTG GAG AGG ATG TTC TTG GGC TTC CCC ACC ACC AAG ACC TAC TTC CCC CAC TTC GAC TTC ACC CAC GGC TCT GAG CAG ATC AAA GCC CAC GGC AAG AAG GTG TCC GAA GCC CTG ACC AAG GCC GTG GGC CAC CTG GAC GAC CTG CCC GGC GCC CTG TCT ACT CTC AGC GAC CTG CAC GCG CAC AAG CTG CGG GTG GAC CCG GTG AAT TTC AAG CTC CTG TCC CAC TGC CTG CTG GTG ACC CTG GCC AAC CAC CAC CCC AGT GAA TTC ACC CCT GCG GTG CAT GCC TCC CTG GAC AAG TTC CTG GCC AAC GTG AGC ACC GTG CTG ACC TCC AAA TAT CGT CTG TCC AGT GAG GAG AAG TCT GCG GTC ACT GCC CTG TGG GGC AAG GTG AAT GTG GAA GAA GTT GGT GGT GAG GCC CTG GGC AGG CTG CTG GTT GTC TAC CCA TGG ACC CAG AGG TTC TTC GAG TCC TTT GGG GAC CTG TCC TCT GCA AAT GCT GTT ATG AAC AAT CCT AAG GTG AAG GCT CAT GGC AAG AAG GTG CTG GCT GCC TTC AGT GAG GGT CTG AGT CAC CTG GAC AAC CTC AAA GGC ACC TTT GCT AAG CTG AGT GAA CTG CAC TGT GAC AAG CTG CAC GTG GAT CCT GAG AAC TTC AGG CTC CTG GGC AAC GTG CTG GTT ATT GTG CTG TCT CAT CAT TTT GGC AAA GAA TTC ACT CCT CAG GTG CAG GCT GCC TAT CAG AAG GTG GTG GCT GGT GTG GCC AAT GCC CTG GCT CAC AAA TAC CAC rat GTG CTC TCT GCA GAT GAC AAA ACC AAC ATC AAG AAC TGC TGG GGG AAG ATT GGT GGC CAT GGT GGT GAA TAT GGC GAG GAG GCC CTA CAG AGG ATG TTC GCT GCC TTC CCC ACC ACC AAG ACC TAC TTC TCT CAC ATT GAT GTA AGC CCC GGC TCT GCC CAG GTC AAG GCT CAC GGC AAG AAG GTT GCT GAT GCC TTG GCC AAA GCT GCA GAC CAC GTC GAA GAC CTG CCT GGT GCC CTG TCC ACT CTG AGC GAC CTG CAT GCC CAC AAA CTG CGT GTG GAT CCT GTC AAC TTC AAG TTC CTG AGC CAC TGC CTG CTG GTG ACC TTG GCT TGC CAC CAC CCT GGA GAT TTC ACA CCC GCC ATG CAC GCC TCT CTG GAC AAA TTC CTT GCC TCT GTG AGC ACT GTG CTG ACC TCC AAG TAC CGT CTA ACT GAT GCT GAG AAG GCT GCT GTT AAT GCC CTG TGG GGA AAG GTG AAC CCT GAT GAT GTT GGT GGC GAG GCC CTG GGC AGG CTG CTG GTT GTC TAC CCT TGG ACC CAG AGG TAC TTT GAT AGC TTT GGG GAC CTG TCC TCT GCC TCT GCT ATC ATG GGT AAC CCT AAG GTG AAG GCC CAT GGC AAG AAG GTG ATA AAC GCC TTC AAT GAT GGC CTG AAA CAC TTG GAC AAC CTC AAG GGC ACC TTT GCT CAT CTG AGT GAA CTC CAC TGT GAC AAG CTG CAT GTG GAT CCT GAG AAC TTC AGG CTC CTG GGC AAT ATG ATT GTG ATT GTG TTG GGC CAC CAC CTG GGC AAG GAA TTC ACC CCC TGT GCA CAG GCT GCC TTC CAG AAG GTG GTG GCT GGA GTG GCC AGT GCC CTG GCT CAC AAG TAC CAC marsupial GTG CTC TCG GAT GCT GAC AAG ACT CAC GTG AAA GCC ATC TGG GGT AAG GTG GGA GGC CAC GCC GGT GCC TAC GCA GCT GAA GCT CTT GCC AGA ACC TTC CTC TCC TTC CCC ACT ACC AAA ACT TAC TTC CCC CAC TTC GAC CTG TCC CCC GGC TCC GCC CAG ATC CAG GGT CAT GGT AAG AAG GTA GCC GAT GCC CTT TCC CAG GCT GTT GCC CAC CTG GAC GAC CTG CCC GGA ACC ATG TCC AAA CTA AGC GAC CTG CAC GCC CAC AAG CTG AGA GTG GAT CCC GTG AAC TTC AAG CTC CTC TCT CAC TGC CTG ATC GTG ACT CTG GCC GCC CAT CTG AGC AAG GAT TTG ACT CCC GAA GTG CAC GCC TCC ATG GAC AAG TTC TTT GCC TCT GTG GCT ACC GTG CTG ACC TCG AAG TAC CGT TTG ACT TCT GAG GAG AAG AAC TGC ATC ACT ACC ATC TGG TCT AAG GTG CAG GTT GAC CAG ACT GGT GGT GAG GCC CTT GGC AGG ATG CTC GTT GTC TAC CCC TGG ACC ACC AGG TTT TTT GGG AGC TTT GGT GAT CTG TCC TCT CCT GGC GCT GTC ATG TCA AAT TCT AAG GTT CAA GCC CAT GGT GCT AAG GTG TTG ACC TCC TTC GGT GAA GCA GTC AAG CAT TTG GAC AAC CTG AAG GGT ACT TAT GCC AAG TTG AGT GAG CTC CAC TGT GAC AAG CTG CAT GTG GAC CCT GAG AAC TTC AAG ATG CTG GGG AAT ATC ATT GTG ATC TGC CTG GCT GAG CAC TTT GGC AAG GAT TTT ACT CCT GAA TGT CAG GTT GCT TGG CAG AAG CTC GTG GCT GGA GTT GCC CAT GCC CTG GCC CAC AAG TAC CAC Printing out site pattern counts 5 669 P human AAA AAA AAA AAC AAC AAC AAC AAC AAC AAC AAC AAC AAG AAG AAG AAG AAG AAG AAG AAG AAG AAT ACA ACC ACC ACC ACC ACC ACC ACC ACC ACT ACT ACT AGC AGC AGC AGC AGG AGG AGG AGT AGT ATG ATG ATG CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAG CAG CAT CAT CCA CCA CCC CCC CCC CCG CCG CCT CCT CCT CCT CCT CCT CCT CGG CGT CTA CTC CTC CTC CTC CTC CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTT GAA GAA GAC GAC GAC GAC GAC GAC GAG GAG GAG GAG GAG GAG GAG GAG GAT GAT GAT GAT GAT GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCG GCG GCG GCG GCG GCG GCG GCT GCT GCT GCT GCT GCT GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC GGG GGT GGT GGT GGT GGT GTC GTC GTC GTC GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTT GTT GTT GTT GTT TAC TAC TAT TAT TAT TCC TCC TCC TCC TCC TCC TCT TCT TCT TCT TGC TGG TGT TGT TTC TTC TTC TTC TTC TTC TTT TTT TTT TTT TTT goat-cow ... ..G ..G ..A ..A ... ... ... ... ..T G.. GGT ... ... ... ... ... ... ... .GA G.. ... G.G ... ... ... ... ... ... ..T T.. ..C ... ... ... ... ... ..T .A. ... ... ... ... ... ... C.. A.. A.T ... ... ... ... ... ..T ..T ..T ... ... ... .GC ..G GTG ... ... ... ..C ... ..C ..C ... ... G.C G.. G.. ..T ... ..G ..A ... ... ... ..T A.. ..A ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. T.. T.T ..G ... ... ... ... ... ... ..T .C. ... ... ... ... ... ... ..T .CT A.. ..C ... ... ... AAT .A. .AT ... ... ... ... ... ... ... ... ... ... ..G ..T ..T ..T T.. TG. A.T ..A ..C ... ... .GC .GC AAG ..C ..C ... ... ... AA. ..A ... ... ... ... ... ... ... ... ... .A. ..C ... ... ... ... ... ... ..G C.. C.. ..C ... ... ... ... ... ... ... ... ..T ..C ..C ... ... ... ... ... ... ... .T. AG. ... ... ... ... ..T AAC G.. ..G ... .C. ... GT. ... ... ... ... ... ... ..T ... ... ... ... ... rabbit ... ... ..G ..G ..T ... ... ..T ..T ... ... GG. ..A ..A ... ... ... ... ... ..A ... ... .AG ... ... ... ... ... ..T ... ... ... T.C T.. .C. ... TC. ... ... ... ... ... ... ... ... C.. ... ..T ... ... ... ... ..T ... ... ... ... ... ... ... ..T .AG ... ... ... ..C ... ..A ... ... ... ..C AG. G.A ... ... ..G ..G .A. ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... G.. T.C T.. ... ... ... ..G ... ... ... ... ... ... ... ..A ..A ... ... ... ... ... ..A ... ..G ..C A.. ..A ... AGT ... A.T A.T .AG ... ... ... ... ..G ..T ..T T.. ... ... ..T T.T ... AA. ..C ..C ... ..C ... AGC .GC AG. ..C ... ... ... .G. AA. ... .AA .C. ... ... ... ... ... ..T ... .C. ..C ... ... ... A.. ... ..G ..T C.. ... ... ... ... ... ... ... ... ... ... ..T A.C ..C A.C ... ... ... ..T ..C ... ... GG. ... ... ... ... ..T AAC ... ... ... ... ... AT. ... ... ... ... ... ... ... ..C ..C ... ... ... rat ..G ..G ..G ..A ... ... ..T ... ... ... ... GGT ... ... ..A ... ... ... ... ... ... .G. CAT ..A ... ... ..T G.. ... ... ... .A. ... T.. ... ... ... ... ... ... ... .A. ... ... ... C.. ..T ... ... ... ..T .C. ... ... ... ..T ... ... ... ..C ..C TGT ... ..T ..T T.T ..T ... ..C ... ... G.A GA. G.C ..T ... ..G A.A .A. ... ... T.. ... A.T T.. ... ..A ..C ... ... ... ... ... ... T.. T.. ..A G.A GCT ... ..T ... ..G ... ..T ..A ... ..T ..T ... ..T ..A C.. ... ... ..T .CT ..T ..A ... ..C TC. ... ... .GA ... A.T AA. ... ... ... ..T TG. ..T .AT ..T ..T ..T ... ..T .G. ... TG. ..C .A. ..C ..C ..C .GC .AC AAA ..C ..C ... ... .G. ..T ..T ..G .CT ..A ... ... ... ..T ... ... AAC ..C ..A ..C ... A.. ... ... ..G ..C .CA A.. A.. CCT .CA ... ... ... ... ..T ..T ..C ... A.. A.C ... ... ... ..C ... .TC G.. AG. ... ... ..T ... ... G.. ... ... ... ... AT. ... A.T .A. ... ... ... ... ..C ... C.G ... ... marsupial ..G ..G ..G C.G C.G ... ..T ... ..T C.. ... GGA ... C.. ... ..A ... C.A GCT ... ... C.. .AG ..T ... ..T ... T.. ..T ... ..T ... ... T.. TC. GCT TCT ... .A. ..A ... G.. ... .CC ... C.. ... ... ... ..T ... .C. ... ... ..T ..T ACC ... ... G.G ..T GA. ... AG. ... ..C ..C ..C ..C ... T.. GA. T.. ... A.A ... ..C T.G ..G A.G ..G ... G.C A.T T.. ..A T.. ..C A.C A.. ..C ... ..T T.. ... ..T ..T ... ..C ... T.T A.C ..G ..T C.G ... ... ... ..T ... ..T ... .CC ..A ... .G. ... ..T .CC ..A ... .GC ..C ..C AAG ..T AAA ... ... A.. ... ... AT. TG. ..T ... ... ..T ..T ... ..T T.. ... A.C ..T ..C ..C .AA .GC ..C AAG ..C ..C ... .T. ..C TCA ..T ..T ..T TCT ... ..G ..T ..A .CA ..T ACC .CA ..A ... ... ..G ... ..G ..G C.. TGT ... A.C ..T ..T C.C ... ..T TGC ..A ..T A.C A.C ..G ..C AC. ... ... ..C ..C .GG ... AG. ... ..G ... ... ... AAC ..C ..G ... ... ATC ... ... ..T ... ..G ..T ... ..C ... ... .A. ... 1 1 2 1 1 1 1 1 1 1 1 1 1 1 3 2 7 1 1 1 1 1 1 1 2 4 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 6 2 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 3 1 6 1 1 2 1 1 1 1 1 1 1 1 1 1 1 4 1 1 2 1 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 2 1 1 1 1 1 1 1 3 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 9 2 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 1 5 1 1 1 1 1 1 1 1 CODONML (in paml version 4.3, August 2009) abglobin.nuc Model: One dN/dS ratio for branches Codon frequency model: F3x4 ns = 5 ls = 285 Codon usage in sequences -------------------------------------------------------------------------------------------------- Phe TTT 5 8 3 3 6 | Ser TCT 4 2 6 7 6 | Tyr TAT 3 2 3 1 1 | Cys TGT 2 1 1 2 2 TTC 10 9 13 11 8 | TCC 6 7 7 3 8 | TAC 3 3 3 5 5 | TGC 1 1 1 3 3 Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 TTG 0 2 1 4 5 | TCG 0 1 0 0 2 | TAG 0 0 0 0 0 | Trp TGG 3 3 3 3 4 -------------------------------------------------------------------------------------------------- Leu CTT 1 1 0 1 3 | Pro CCT 7 2 4 7 3 | His CAT 2 4 4 5 6 | Arg CGT 1 2 1 2 1 CTC 5 4 4 4 7 | CCC 3 6 5 4 7 | CAC 16 11 15 14 12 | CGC 0 1 0 0 0 CTA 1 2 0 2 1 | CCA 2 0 1 0 0 | Gln CAA 0 0 0 0 1 | CGA 0 0 0 0 0 CTG 29 28 30 21 15 | CCG 2 2 1 0 0 | CAG 4 4 5 5 7 | CGG 1 0 1 0 0 -------------------------------------------------------------------------------------------------- Ile ATT 0 0 1 4 1 | Thr ACT 3 4 4 3 10 | Asn AAT 1 5 5 3 2 | Ser AGT 2 3 5 2 1 ATC 0 0 3 2 7 | ACC 12 11 12 9 9 | AAC 9 7 7 8 4 | AGC 4 4 3 5 3 ATA 0 0 0 1 0 | ACA 1 0 0 1 0 | Lys AAA 4 3 5 5 3 | Arg AGA 0 1 0 0 2 Met ATG 3 3 2 4 5 | ACG 0 0 0 0 0 | AAG 18 21 19 19 21 | AGG 4 3 4 4 2 -------------------------------------------------------------------------------------------------- Val GTT 5 5 4 4 6 | Ala GCT 8 11 8 13 10 | Asp GAT 5 8 1 11 6 | Gly GGT 5 4 5 6 10 GTC 4 6 2 4 3 | GCC 21 18 16 18 19 | GAC 10 10 10 8 10 | GGC 14 15 14 12 5 GTA 0 0 0 1 1 | GCA 0 1 1 3 2 | Glu GAA 2 2 7 4 4 | GGA 0 1 0 3 3 GTG 21 19 21 14 14 | GCG 7 4 3 0 0 | GAG 10 9 10 5 6 | GGG 1 1 1 2 2 -------------------------------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: human position 1: T:0.12982 C:0.25965 A:0.21404 G:0.39649 position 2: T:0.29474 C:0.26667 A:0.30526 G:0.13333 position 3: T:0.18947 C:0.41404 A:0.03509 G:0.36140 Average T:0.20468 C:0.31345 A:0.18480 G:0.29708 #2: goat-cow position 1: T:0.13684 C:0.23509 A:0.22807 G:0.40000 position 2: T:0.30526 C:0.24211 A:0.31228 G:0.14035 position 3: T:0.21754 C:0.39649 A:0.03509 G:0.35088 Average T:0.21988 C:0.29123 A:0.19181 G:0.29708 #3: rabbit position 1: T:0.14386 C:0.24912 A:0.24561 G:0.36140 position 2: T:0.29474 C:0.23860 A:0.32982 G:0.13684 position 3: T:0.19298 C:0.40351 A:0.04912 G:0.35439 Average T:0.21053 C:0.29708 A:0.20819 G:0.28421 #4: rat position 1: T:0.14737 C:0.22807 A:0.24561 G:0.37895 position 2: T:0.28070 C:0.23860 A:0.32632 G:0.15439 position 3: T:0.25965 C:0.38596 A:0.07018 G:0.28421 Average T:0.22924 C:0.28421 A:0.21404 G:0.27251 #5: marsupial position 1: T:0.17895 C:0.22105 A:0.24561 G:0.35439 position 2: T:0.28772 C:0.27018 A:0.30877 G:0.13333 position 3: T:0.25965 C:0.38596 A:0.06316 G:0.29123 Average T:0.24211 C:0.29240 A:0.20585 G:0.25965 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 25 | Ser S TCT 25 | Tyr Y TAT 10 | Cys C TGT 8 TTC 51 | TCC 31 | TAC 19 | TGC 9 Leu L TTA 0 | TCA 1 | *** * TAA 0 | *** * TGA 0 TTG 12 | TCG 3 | TAG 0 | Trp W TGG 16 ------------------------------------------------------------------------------ Leu L CTT 6 | Pro P CCT 23 | His H CAT 21 | Arg R CGT 7 CTC 24 | CCC 25 | CAC 68 | CGC 1 CTA 6 | CCA 3 | Gln Q CAA 1 | CGA 0 CTG 123 | CCG 5 | CAG 25 | CGG 2 ------------------------------------------------------------------------------ Ile I ATT 6 | Thr T ACT 24 | Asn N AAT 16 | Ser S AGT 13 ATC 12 | ACC 53 | AAC 35 | AGC 19 ATA 1 | ACA 2 | Lys K AAA 20 | Arg R AGA 3 Met M ATG 17 | ACG 0 | AAG 98 | AGG 17 ------------------------------------------------------------------------------ Val V GTT 24 | Ala A GCT 50 | Asp D GAT 31 | Gly G GGT 30 GTC 19 | GCC 92 | GAC 48 | GGC 60 GTA 2 | GCA 7 | Glu E GAA 19 | GGA 7 GTG 89 | GCG 14 | GAG 40 | GGG 7 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.14737 C:0.23860 A:0.23579 G:0.37825 position 2: T:0.29263 C:0.25123 A:0.31649 G:0.13965 position 3: T:0.22386 C:0.39719 A:0.05053 G:0.32842 Average T:0.22129 C:0.29567 A:0.20094 G:0.28211 Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): 0.00983798 0.01745548 0.00222048 0.01443315 0.00844604 0.01498576 0.00190632 0.01239105 0.01064012 0.01887870 0.00000000 0.00000000 0.00469486 0.00833007 0.00000000 0.00688776 0.01592816 0.02826125 0.00359507 0.02336796 0.01367453 0.02426265 0.00308642 0.02006170 0.01722686 0.03056552 0.00388819 0.02527326 0.00760121 0.01348678 0.00171563 0.01115161 0.01574077 0.02792876 0.00355278 0.02309304 0.01351366 0.02397721 0.00305010 0.01982568 0.01702419 0.03020593 0.00384245 0.02497593 0.00751178 0.01332811 0.00169545 0.01102042 0.02525082 0.04480239 0.00569924 0.03704508 0.02167816 0.03846344 0.00489288 0.03180369 0.02730964 0.04845534 0.00616393 0.04006555 0.01205015 0.02138052 0.00271978 0.01767859 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) human goat-cow 0.2507 (0.0863 0.3443) rabbit 0.2627 (0.0867 0.3301) 0.2943 (0.1054 0.3581) rat 0.2045 (0.1261 0.6164) 0.2462 (0.1493 0.6065) 0.2178 (0.1348 0.6187) marsupial 0.1902 (0.1931 1.0148) 0.1891 (0.1910 1.0099) 0.2184 (0.2111 0.9668) 0.2716 (0.2404 0.8852) pairwise comparison, codon frequencies: F3x4. 2 (goat-cow) ... 1 (human) lnL =-1508.607268 0.47825 2.29137 0.19479 t= 0.4783 S= 186.0 N= 669.0 dN/dS= 0.1948 dN= 0.0839 dS= 0.4309 3 (rabbit) ... 1 (human) lnL =-1512.583367 0.46755 2.19039 0.19819 t= 0.4676 S= 179.9 N= 675.1 dN/dS= 0.1982 dN= 0.0842 dS= 0.4247 3 (rabbit) ... 2 (goat-cow) lnL =-1557.337680 0.53837 2.26427 0.22670 t= 0.5384 S= 183.5 N= 671.5 dN/dS= 0.2267 dN= 0.1036 dS= 0.4570 4 (rat) ... 1 (human) lnL =-1649.727994 0.82576 1.78920 0.15108 t= 0.8258 S= 190.2 N= 664.8 dN/dS= 0.1511 dN= 0.1223 dS= 0.8097 4 (rat) ... 2 (goat-cow) lnL =-1677.101606 0.88091 2.40576 0.18757 t= 0.8809 S= 200.2 N= 654.8 dN/dS= 0.1876 dN= 0.1458 dS= 0.7773 4 (rat) ... 3 (rabbit) lnL =-1666.440696 0.85281 2.21652 0.16114 t= 0.8528 S= 193.2 N= 661.8 dN/dS= 0.1611 dN= 0.1306 dS= 0.8105 5 (marsupial) ... 1 (human) lnL =-1769.079306 2.29076 0.98664 0.05689 t= 2.2908 S= 176.2 N= 678.8 dN/dS= 0.0569 dN= 0.1729 dS= 3.0396 5 (marsupial) ... 2 (goat-cow) lnL =-1774.766235 1.80490 1.19637 0.08052 t= 1.8049 S= 180.8 N= 674.2 dN/dS= 0.0805 dN= 0.1762 dS= 2.1879 5 (marsupial) ... 3 (rabbit) lnL =-1794.595175 2.09984 1.06589 0.06930 t= 2.0998 S= 173.1 N= 681.9 dN/dS= 0.0693 dN= 0.1882 dS= 2.7162 5 (marsupial) ... 4 (rat) lnL =-1842.638722 1.66307 1.02118 0.12318 t= 1.6631 S= 180.6 N= 674.4 dN/dS= 0.1232 dN= 0.2214 dS= 1.7973 Bio-Tools-Phylo-PAML-1.7.3/t/data/branchSite.mlc0000644000175000017500000001263113316145226022112 0ustar carandraugcarandraugCODONML (in paml 3.15, November 2005) test.phy Model: several dN/dS ratios for branches Codon frequencies: F3x4 Site-class models: discrete (4 categories) ns = 3 ls = 6 Codon usage in sequences -------------------------------------------------------------------------- Phe TTT 1 1 1 | Ser TCT 1 1 0 | Tyr TAT 0 0 0 | Cys TGT 0 0 0 TTC 0 0 0 | TCC 0 0 1 | TAC 0 0 0 | TGC 0 0 0 Leu TTA 0 0 0 | TCA 0 0 0 | *** TAA 0 0 0 | *** TGA 0 0 0 TTG 0 0 0 | TCG 0 0 0 | TAG 0 0 0 | Trp TGG 0 0 0 -------------------------------------------------------------------------- Leu CTT 0 0 0 | Pro CCT 0 0 0 | His CAT 1 1 1 | Arg CGT 0 0 0 CTC 0 0 0 | CCC 0 0 1 | CAC 0 0 0 | CGC 0 0 0 CTA 0 0 0 | CCA 1 1 0 | Gln CAA 0 0 0 | CGA 0 0 0 CTG 0 0 0 | CCG 0 0 0 | CAG 0 0 0 | CGG 0 0 0 -------------------------------------------------------------------------- Ile ATT 0 0 0 | Thr ACT 0 0 0 | Asn AAT 0 0 0 | Ser AGT 0 0 0 ATC 0 0 0 | ACC 0 0 0 | AAC 0 0 0 | AGC 0 0 0 ATA 0 0 0 | ACA 0 0 0 | Lys AAA 0 0 0 | Arg AGA 0 0 0 Met ATG 2 1 1 | ACG 0 1 1 | AAG 0 0 0 | AGG 0 0 0 -------------------------------------------------------------------------- Val GTT 0 0 0 | Ala GCT 0 0 0 | Asp GAT 0 0 0 | Gly GGT 0 0 0 GTC 0 0 0 | GCC 0 0 0 | GAC 0 0 0 | GGC 0 0 0 GTA 0 0 0 | GCA 0 0 0 | Glu GAA 0 0 0 | GGA 0 0 0 GTG 0 0 0 | GCG 0 0 0 | GAG 0 0 0 | GGG 0 0 0 -------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: test0 position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 position 2: T:0.50000 C:0.33333 A:0.16667 G:0.00000 position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333 #2: test1 position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000 position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333 #3: test2 position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000 position 3: T:0.33333 C:0.33333 A:0.00000 G:0.33333 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 3 | Ser S TCT 2 | Tyr Y TAT 0 | Cys C TGT 0 TTC 0 | TCC 1 | TAC 0 | TGC 0 Leu L TTA 0 | TCA 0 | *** * TAA 0 | *** * TGA 0 TTG 0 | TCG 0 | TAG 0 | Trp W TGG 0 ------------------------------------------------------------------------------ Leu L CTT 0 | Pro P CCT 0 | His H CAT 3 | Arg R CGT 0 CTC 0 | CCC 1 | CAC 0 | CGC 0 CTA 0 | CCA 2 | Gln Q CAA 0 | CGA 0 CTG 0 | CCG 0 | CAG 0 | CGG 0 ------------------------------------------------------------------------------ Ile I ATT 0 | Thr T ACT 0 | Asn N AAT 0 | Ser S AGT 0 ATC 0 | ACC 0 | AAC 0 | AGC 0 ATA 0 | ACA 0 | Lys K AAA 0 | Arg R AGA 0 Met M ATG 4 | ACG 2 | AAG 0 | AGG 0 ------------------------------------------------------------------------------ Val V GTT 0 | Ala A GCT 0 | Asp D GAT 0 | Gly G GGT 0 GTC 0 | GCC 0 | GAC 0 | GGC 0 GTA 0 | GCA 0 | Glu E GAA 0 | GGA 0 GTG 0 | GCG 0 | GAG 0 | GGG 0 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 position 2: T:0.38889 C:0.44444 A:0.16667 G:0.00000 position 3: T:0.44444 C:0.11111 A:0.11111 G:0.33333 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) test0 test1 -1.0000 (0.0706 0.0000) test2 0.0510 (0.0706 1.3844) 0.0000 (0.0000 0.9745) TREE # 1: (1, 2, 3); MP score: 3 lnL(ntime: 3 np: 9): -28.298935 +0.000000 4..1 4..2 4..3 0.31500 0.00000 18.45220 99.00000 0.00000 0.65968 0.00000 0.00000 999.00000 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 18.76720 (1: 0.314996, 2: 0.000004, 3: 18.452204); (test0: 0.314996, test1: 0.000004, test2: 18.452204); Detailed output identifying parameters kappa (ts/tv) = 99.00000 dN/dS for site classes (K=4) site class 0 1 2a 2b proportion 0.00000 0.65968 0.00000 0.34032 background w 0.00000 0.00000 0.00000 0.00000 foreground w 0.00000 0.00000999.00000 999.00000 Naive Empirical Bayes (NEB) analysis (please use the BEB results.) Positive sites for foreground lineages Prob(w>1): 2 M 1.000** Bio-Tools-Phylo-PAML-1.7.3/t/data/baseml.usertree0000644000175000017500000000227113316145226022355 0ustar carandraugcarandraug seed used = 30455833 BASEML (in paml 3.14, January 2004) m.phy HKY85 dGamma (ncatG=5) ns = 3 ls = 57 # site patterns = 12 7 16 15 1 3 2 1 1 8 1 1 1 wih99_snap GTAGAGTACT TT wm276_snap ...AGAG..G A. jec21_snap ....GACT.. CC Frequencies.. T C A G wih99_snap 0.3509 0.1404 0.3333 0.1754 wm276_snap 0.2982 0.1404 0.3509 0.2105 jec21_snap 0.3158 0.1930 0.2982 0.1930 Average 0.3216 0.1579 0.3275 0.1930 # constant sites: 46 (80.70%) ln Lmax (unconstrained) = -110.532715 Distances:HKY85 (kappa) (alpha set at 0.50) This matrix is not used in later m.l. analysis. wih99_snap wm276_snap 0.3240( 9.3595) jec21_snap 0.2974(33.1197) 0.1343( 1.1101) TREE # 1: (2, 3, 1); MP score: 13.00 lnL(ntime: 3 np: 3): -129.328757 +0.000000 4..2 4..3 4..1 0.08669 0.05274 0.15105 tree length = 0.29048 (wm276_snap, jec21_snap, wih99_snap); (wm276_snap: 0.086692, jec21_snap: 0.052740, wih99_snap: 0.151050); Bio-Tools-Phylo-PAML-1.7.3/t/data/test 2.txt0000644000175000017500000000107513316145226021175 0ustar carandraugcarandraug>Test AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTBio-Tools-Phylo-PAML-1.7.3/t/data/singleNSsite.mlc0000644000175000017500000001532113316145226022436 0ustar carandraugcarandraugCODONML (in paml 3.15, November 2005) test.phy Model: One dN/dS ratio Codon frequencies: F3x4 Site-class models: PositiveSelection ns = 3 ls = 6 Codon usage in sequences -------------------------------------------------------------------------- Phe TTT 1 1 1 | Ser TCT 1 1 0 | Tyr TAT 0 0 0 | Cys TGT 0 0 0 TTC 0 0 0 | TCC 0 0 1 | TAC 0 0 0 | TGC 0 0 0 Leu TTA 0 0 0 | TCA 0 0 0 | *** TAA 0 0 0 | *** TGA 0 0 0 TTG 0 0 0 | TCG 0 0 0 | TAG 0 0 0 | Trp TGG 0 0 0 -------------------------------------------------------------------------- Leu CTT 0 0 0 | Pro CCT 0 0 0 | His CAT 1 1 1 | Arg CGT 0 0 0 CTC 0 0 0 | CCC 0 0 1 | CAC 0 0 0 | CGC 0 0 0 CTA 0 0 0 | CCA 1 1 0 | Gln CAA 0 0 0 | CGA 0 0 0 CTG 0 0 0 | CCG 0 0 0 | CAG 0 0 0 | CGG 0 0 0 -------------------------------------------------------------------------- Ile ATT 0 0 0 | Thr ACT 0 0 0 | Asn AAT 0 0 0 | Ser AGT 0 0 0 ATC 0 0 0 | ACC 0 0 0 | AAC 0 0 0 | AGC 0 0 0 ATA 0 0 0 | ACA 0 0 0 | Lys AAA 0 0 0 | Arg AGA 0 0 0 Met ATG 2 1 1 | ACG 0 1 1 | AAG 0 0 0 | AGG 0 0 0 -------------------------------------------------------------------------- Val GTT 0 0 0 | Ala GCT 0 0 0 | Asp GAT 0 0 0 | Gly GGT 0 0 0 GTC 0 0 0 | GCC 0 0 0 | GAC 0 0 0 | GGC 0 0 0 GTA 0 0 0 | GCA 0 0 0 | Glu GAA 0 0 0 | GGA 0 0 0 GTG 0 0 0 | GCG 0 0 0 | GAG 0 0 0 | GGG 0 0 0 -------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: test0 position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 position 2: T:0.50000 C:0.33333 A:0.16667 G:0.00000 position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333 #2: test1 position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000 position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333 #3: test2 position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000 position 3: T:0.33333 C:0.33333 A:0.00000 G:0.33333 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 3 | Ser S TCT 2 | Tyr Y TAT 0 | Cys C TGT 0 TTC 0 | TCC 1 | TAC 0 | TGC 0 Leu L TTA 0 | TCA 0 | *** * TAA 0 | *** * TGA 0 TTG 0 | TCG 0 | TAG 0 | Trp W TGG 0 ------------------------------------------------------------------------------ Leu L CTT 0 | Pro P CCT 0 | His H CAT 3 | Arg R CGT 0 CTC 0 | CCC 1 | CAC 0 | CGC 0 CTA 0 | CCA 2 | Gln Q CAA 0 | CGA 0 CTG 0 | CCG 0 | CAG 0 | CGG 0 ------------------------------------------------------------------------------ Ile I ATT 0 | Thr T ACT 0 | Asn N AAT 0 | Ser S AGT 0 ATC 0 | ACC 0 | AAC 0 | AGC 0 ATA 0 | ACA 0 | Lys K AAA 0 | Arg R AGA 0 Met M ATG 4 | ACG 2 | AAG 0 | AGG 0 ------------------------------------------------------------------------------ Val V GTT 0 | Ala A GCT 0 | Asp D GAT 0 | Gly G GGT 0 GTC 0 | GCC 0 | GAC 0 | GGC 0 GTA 0 | GCA 0 | Glu E GAA 0 | GGA 0 GTG 0 | GCG 0 | GAG 0 | GGG 0 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 position 2: T:0.38889 C:0.44444 A:0.16667 G:0.00000 position 3: T:0.44444 C:0.11111 A:0.11111 G:0.33333 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) test0 test1 -1.0000 (0.0706 0.0000) test2 0.0510 (0.0706 1.3844) 0.0000 (0.0000 0.9745) TREE # 1: (1, 2, 3); MP score: 3 check convergence.. lnL(ntime: 3 np: 8): -30.819156 +0.000000 4..1 4..2 4..3 0.25573 0.00000 0.62424 5.28487 1.00000 0.00000 0.09213 1.00000 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 0.87997 (1: 0.255727, 2: 0.000004, 3: 0.624239); (test0: 0.255727, test1: 0.000004, test2: 0.624239); Detailed output identifying parameters kappa (ts/tv) = 5.28487 dN/dS for site classes (K=3) p: 1.00000 0.00000 0.00000 w: 0.09213 1.00000 1.00000 dN & dS for each branch branch t N S dN/dS dN dS N*dN S*dS 4..1 0.256 12.9 5.1 0.0921 0.0224 0.2429 0.3 1.2 4..2 0.000 12.9 5.1 0.0921 0.0000 0.0000 0.0 0.0 4..3 0.624 12.9 5.1 0.0921 0.0546 0.5930 0.7 3.0 Naive Empirical Bayes (NEB) analysis Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) Positively selected sites (*: P>95%; **: P>99%) Pr(w>1) post mean +- SE for w The grid (see ternary graph for p0-p1) w0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950 w2: 1.500 2.500 3.500 4.500 5.500 6.500 7.500 8.500 9.500 10.500 Posterior on the grid w0: 0.402 0.260 0.147 0.081 0.045 0.026 0.016 0.010 0.007 0.005 w2: 0.138 0.114 0.104 0.098 0.095 0.093 0.091 0.090 0.089 0.088 Posterior for p0-p1 (see the ternary graph) 0.001 0.001 0.002 0.003 0.001 0.001 0.002 0.003 0.006 0.000 0.001 0.001 0.002 0.004 0.006 0.010 0.000 0.000 0.001 0.001 0.003 0.004 0.007 0.011 0.016 0.000 0.000 0.001 0.001 0.002 0.003 0.005 0.008 0.012 0.017 0.025 0.000 0.000 0.000 0.001 0.001 0.002 0.004 0.006 0.009 0.013 0.019 0.026 0.036 0.000 0.000 0.000 0.000 0.001 0.001 0.003 0.004 0.006 0.009 0.014 0.019 0.027 0.037 0.049 0.000 0.000 0.000 0.000 0.001 0.001 0.002 0.003 0.005 0.007 0.010 0.014 0.020 0.028 0.037 0.049 0.063 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.002 0.003 0.005 0.007 0.010 0.015 0.020 0.027 0.036 0.046 0.061 0.075 sum of density on p0-p1 = 1.000000 Bio-Tools-Phylo-PAML-1.7.3/t/data/codeml45.mlc0000644000175000017500000011043613316145226021446 0ustar carandraugcarandraug 9 1425 Pdel181_DNA2 ATG TCA CCA CAA ACA GAG ACT AAA ACA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAG TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT ACT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATG CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG Pfre186_DNA2 ATG TCA CCA CAA ACA GAG ACT AAA ACA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAG TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT ACT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATG CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT ATT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG Pgra187_DNA2 ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT ACT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG ACT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATG AAA AGG GCT ATA TTT GCC AGA GAA TTG GGA GTT CCT ATT GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCT GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATA AAA TTT GAA TTC GAA GCA ATG GAT ACG TTG Phet26_DNA21 ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTA CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG Pmex37_DNA21 ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT ACT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATG CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT ATT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG Ptre197_DNA2 ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT ACT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG ACT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATG AAA AGG GCT ATA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCT GGT GCT GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC GAA GCA ATG GAT ACG TTG WHR1_DNA225 ATG TCA CCA CAA ACA GAG ACT AAA GCG GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAG TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCC GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT ACT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATG AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG YALD273_DNA5 ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTA CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG Pop_trich_ch ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTA CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG Printing out site pattern counts 9 225 P Pdel181_DNA2 AAA AAC AAG AAT ACA ACA ACC ACG ACT ACT AGA AGC AGG AGT ATA ATC ATC ATC ATG ATG ATT ATT CAA CAA CAC CAG CAT CCA CCC CCC CCG CCT CCT CGA CGC CGT CTA CTG CTG CTT GAA GAC GAG GAG GAT GCA GCC GCC GCT GCT GGA GGC GGG GGT GTA GTA GTC GTG GTT GTT GTT TAC TAT TCA TCC TCG TCT TCT TGC TGG TGT TTA TTC TTG TTT Pfre186_DNA2 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... Pgra187_DNA2 ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ..G ..T ..A ... ..A ... ... G.. ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... A.. ... ... ... ... ... A.. ... ... ... ... AC. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... Phet26_DNA21 ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... Pmex37_DNA21 ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... Ptre197_DNA2 ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ..G ... ..A ... ... ... ... G.. ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ..T A.. ... ... ... ... ... A.. ... ... ... ... AC. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... WHR1_DNA225 ... ... ... ... ... G.G ... ... ... .G. ... ... ... ... ... ... ..G ... ..A ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... YALD273_DNA5 ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... Pop_trich_ch ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 18 6 6 9 5 1 8 1 16 1 6 3 1 1 1 7 1 1 1 9 1 9 9 1 5 2 9 3 5 1 2 1 10 6 5 11 9 1 3 9 24 5 1 9 22 15 4 1 1 23 13 2 9 23 1 12 1 4 1 1 13 4 13 1 4 1 1 5 3 8 5 9 8 10 14 CODONML (in paml version 4.5, December 2011) examples/small_taxon_set.nuc Model: One dN/dS ratio for branches Codon frequency model: F3x4 ns = 9 ls = 475 Codon usage in sequences -------------------------------------------------------------------------------------------------------------- Phe TTT 14 14 14 14 14 14 | Ser TCT 6 6 6 6 6 6 | Tyr TAT 13 13 13 13 13 13 | Cys TGT 5 5 5 5 5 5 TTC 8 8 8 8 8 8 | TCC 4 4 4 4 4 4 | TAC 4 4 4 4 4 4 | TGC 3 3 3 3 3 3 Leu TTA 9 9 9 9 9 9 | TCA 1 1 1 1 1 1 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 TTG 10 10 10 10 10 10 | TCG 1 1 1 1 1 1 | TAG 0 0 0 0 0 0 | Trp TGG 8 8 8 8 8 8 -------------------------------------------------------------------------------------------------------------- Leu CTT 9 9 9 9 9 9 | Pro CCT 11 11 12 11 10 12 | His CAT 9 9 9 9 9 9 | Arg CGT 11 11 11 11 11 11 CTC 0 0 0 0 0 0 | CCC 6 6 5 6 6 5 | CAC 5 5 5 5 5 5 | CGC 5 5 5 5 5 5 CTA 9 9 9 10 9 9 | CCA 3 3 3 3 3 3 | Gln CAA 10 10 9 10 10 9 | CGA 6 6 6 6 6 6 CTG 4 4 4 3 4 4 | CCG 2 2 2 2 2 2 | CAG 2 2 2 2 2 2 | CGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------- Ile ATT 10 11 10 10 11 10 | Thr ACT 17 17 18 16 17 18 | Asn AAT 9 9 9 9 9 9 | Ser AGT 1 1 2 2 2 2 ATC 9 9 7 9 9 8 | ACC 8 8 8 8 8 8 | AAC 6 6 6 6 6 6 | AGC 3 3 3 3 3 3 ATA 1 1 4 2 1 3 | ACA 6 6 5 5 5 5 | Lys AAA 18 18 18 18 18 18 | Arg AGA 6 6 6 6 6 6 Met ATG 10 10 10 9 10 10 | ACG 1 1 1 1 1 1 | AAG 6 6 6 6 6 6 | AGG 1 1 1 1 1 1 -------------------------------------------------------------------------------------------------------------- Val GTT 15 14 14 15 14 14 | Ala GCT 24 24 23 24 24 24 | Asp GAT 22 22 22 22 22 22 | Gly GGT 23 23 23 23 23 23 GTC 1 1 1 1 1 1 | GCC 5 5 5 5 5 4 | GAC 5 5 6 6 6 6 | GGC 2 2 2 2 2 2 GTA 13 13 12 13 13 12 | GCA 15 15 16 16 16 16 | Glu GAA 24 24 25 24 24 25 | GGA 13 13 13 13 13 13 GTG 4 4 4 4 4 4 | GCG 0 0 0 0 0 0 | GAG 10 10 9 9 9 9 | GGG 9 9 9 9 9 9 -------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------- Phe TTT 14 14 14 | Ser TCT 5 6 6 | Tyr TAT 13 13 13 | Cys TGT 5 5 5 TTC 8 8 8 | TCC 5 4 4 | TAC 4 4 4 | TGC 3 3 3 Leu TTA 9 9 9 | TCA 1 1 1 | *** TAA 0 0 0 | *** TGA 0 0 0 TTG 10 10 10 | TCG 1 1 1 | TAG 0 0 0 | Trp TGG 8 8 8 -------------------------------------------------------------------------- Leu CTT 9 9 9 | Pro CCT 10 11 11 | His CAT 9 9 9 | Arg CGT 11 11 11 CTC 0 0 0 | CCC 6 6 6 | CAC 5 5 5 | CGC 5 5 5 CTA 9 10 10 | CCA 3 3 3 | Gln CAA 10 10 10 | CGA 6 6 6 CTG 4 3 3 | CCG 2 2 2 | CAG 2 2 2 | CGG 0 0 0 -------------------------------------------------------------------------- Ile ATT 10 10 10 | Thr ACT 17 16 16 | Asn AAT 9 9 9 | Ser AGT 2 2 2 ATC 8 9 9 | ACC 8 8 8 | AAC 6 6 6 | AGC 3 3 3 ATA 2 2 2 | ACA 5 5 5 | Lys AAA 18 18 18 | Arg AGA 6 6 6 Met ATG 10 9 9 | ACG 1 1 1 | AAG 6 6 6 | AGG 1 1 1 -------------------------------------------------------------------------- Val GTT 15 15 15 | Ala GCT 24 24 24 | Asp GAT 22 22 22 | Gly GGT 23 23 23 GTC 1 1 1 | GCC 5 5 5 | GAC 5 6 6 | GGC 2 2 2 GTA 13 13 13 | GCA 15 16 16 | Glu GAA 24 24 24 | GGA 13 13 13 GTG 4 4 4 | GCG 1 0 0 | GAG 10 9 9 | GGG 9 9 9 -------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: Pdel181_DNA2 position 1: T:0.18105 C:0.19368 A:0.23579 G:0.38947 position 2: T:0.26526 C:0.23158 A:0.30105 G:0.20211 position 3: T:0.41895 C:0.15579 A:0.28211 G:0.14316 Average T:0.28842 C:0.19368 A:0.27298 G:0.24491 #2: Pfre186_DNA2 position 1: T:0.18105 C:0.19368 A:0.23789 G:0.38737 position 2: T:0.26526 C:0.23158 A:0.30105 G:0.20211 position 3: T:0.41895 C:0.15579 A:0.28211 G:0.14316 Average T:0.28842 C:0.19368 A:0.27368 G:0.24421 #3: Pgra187_DNA2 position 1: T:0.18105 C:0.19158 A:0.24000 G:0.38737 position 2: T:0.26316 C:0.23158 A:0.30105 G:0.20421 position 3: T:0.42105 C:0.15158 A:0.28632 G:0.14105 Average T:0.28842 C:0.19158 A:0.27579 G:0.24421 #4: Phet26_DNA21 position 1: T:0.18105 C:0.19368 A:0.23368 G:0.39158 position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 position 3: T:0.41895 C:0.15789 A:0.28632 G:0.13684 Average T:0.28842 C:0.19368 A:0.27368 G:0.24421 #5: Pmex37_DNA21 position 1: T:0.18105 C:0.19158 A:0.23789 G:0.38947 position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 position 3: T:0.41895 C:0.15789 A:0.28211 G:0.14105 Average T:0.28842 C:0.19298 A:0.27368 G:0.24491 #6: Ptre197_DNA2 position 1: T:0.18105 C:0.19158 A:0.24000 G:0.38737 position 2: T:0.26316 C:0.23158 A:0.30105 G:0.20421 position 3: T:0.42316 C:0.15158 A:0.28421 G:0.14105 Average T:0.28912 C:0.19158 A:0.27509 G:0.24421 #7: WHR1_DNA225 position 1: T:0.18105 C:0.19158 A:0.23579 G:0.39158 position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 position 3: T:0.41684 C:0.15579 A:0.28211 G:0.14526 Average T:0.28772 C:0.19228 A:0.27298 G:0.24702 #8: YALD273_DNA5 position 1: T:0.18105 C:0.19368 A:0.23368 G:0.39158 position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 position 3: T:0.41895 C:0.15789 A:0.28632 G:0.13684 Average T:0.28842 C:0.19368 A:0.27368 G:0.24421 #9: Pop_trich_ch position 1: T:0.18105 C:0.19368 A:0.23368 G:0.39158 position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 position 3: T:0.41895 C:0.15789 A:0.28632 G:0.13684 Average T:0.28842 C:0.19368 A:0.27368 G:0.24421 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 126 | Ser S TCT 53 | Tyr Y TAT 117 | Cys C TGT 45 TTC 72 | TCC 37 | TAC 36 | TGC 27 Leu L TTA 81 | TCA 9 | *** * TAA 0 | *** * TGA 0 TTG 90 | TCG 9 | TAG 0 | Trp W TGG 72 ------------------------------------------------------------------------------ Leu L CTT 81 | Pro P CCT 99 | His H CAT 81 | Arg R CGT 99 CTC 0 | CCC 52 | CAC 45 | CGC 45 CTA 84 | CCA 27 | Gln Q CAA 88 | CGA 54 CTG 33 | CCG 18 | CAG 18 | CGG 0 ------------------------------------------------------------------------------ Ile I ATT 92 | Thr T ACT 152 | Asn N AAT 81 | Ser S AGT 16 ATC 77 | ACC 72 | AAC 54 | AGC 27 ATA 18 | ACA 47 | Lys K AAA 162 | Arg R AGA 54 Met M ATG 87 | ACG 9 | AAG 54 | AGG 9 ------------------------------------------------------------------------------ Val V GTT 131 | Ala A GCT 215 | Asp D GAT 198 | Gly G GGT 207 GTC 9 | GCC 44 | GAC 51 | GGC 18 GTA 115 | GCA 141 | Glu E GAA 218 | GGA 117 GTG 36 | GCG 1 | GAG 84 | GGG 81 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.18105 C:0.19275 A:0.23649 G:0.38971 position 2: T:0.26480 C:0.23041 A:0.30105 G:0.20374 position 3: T:0.41942 C:0.15579 A:0.28421 G:0.14058 Average T:0.28842 C:0.19298 A:0.27392 G:0.24468 Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): 0.02080748 0.00772882 0.01409988 0.00697451 0.01810545 0.00672517 0.01226889 0.00606881 0.02365656 0.00878710 0.00000000 0.00000000 0.01601000 0.00594683 0.00000000 0.00536643 0.02215163 0.00822810 0.01501073 0.00742506 0.01927505 0.00715961 0.01306145 0.00646085 0.02518476 0.00935474 0.01706608 0.00844174 0.01704423 0.00633099 0.01154977 0.00571310 0.02717876 0.01009540 0.01841729 0.00911012 0.02364937 0.00878443 0.01602564 0.00792709 0.03090024 0.01147772 0.02093909 0.01035753 0.02091228 0.00776775 0.01417090 0.00700964 0.04478716 0.01663594 0.03034936 0.01501232 0.03897116 0.01447562 0.02640823 0.01306284 0.05091968 0.01891383 0.03450497 0.01706789 0.03446079 0.01280027 0.02335185 0.01155100 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later ML. analysis. Use runmode = -2 for ML pairwise comparison.) Pdel181_DNA2 Pfre186_DNA2 -1.0000 (0.0009 0.0000) Pgra187_DNA2 1.0623 (0.0093 0.0088) 1.1684 (0.0102 0.0088) Phet26_DNA21 1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117) Pmex37_DNA21 -1.0000 (0.0046 0.0000)-1.0000 (0.0037 0.0000) 0.9534 (0.0084 0.0088) 0.9555 (0.0028 0.0029) Ptre197_DNA2 1.5965 (0.0093 0.0058) 1.7561 (0.0102 0.0058) 0.0000 (0.0000 0.0088) 0.6357 (0.0056 0.0088) 1.4328 (0.0084 0.0058) WHR1_DNA225 0.7964 (0.0046 0.0058) 0.9557 (0.0056 0.0058) 0.4430 (0.0065 0.0147) 0.3175 (0.0028 0.0088) 0.6354 (0.0037 0.0058) 0.5548 (0.0065 0.0117) YALD273_DNA5 1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117)-1.0000 (0.0000 0.0000) 0.9555 (0.0028 0.0029) 0.6357 (0.0056 0.0088) 0.3175 (0.0028 0.0088) Pop_trich_ch 1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117)-1.0000 (0.0000 0.0000) 0.9555 (0.0028 0.0029) 0.6357 (0.0056 0.0088) 0.3175 (0.0028 0.0088)-1.0000 (0.0000 0.0000) pairwise comparison, codon frequencies: F3x4. 2 (Pfre186_DNA2) ... 1 (Pdel181_DNA2) lnL =-1891.391969 0.00214 999.00000 99.00000 t= 0.0021 S= 396.3 N= 1028.7 dN/dS= 99.0000 dN = 0.0010 dS = 0.0000 3 (Pgra187_DNA2) ... 1 (Pdel181_DNA2) lnL =-1968.029688 0.02808 3.26389 0.98370 t= 0.0281 S= 341.7 N= 1083.3 dN/dS= 0.9837 dN = 0.0093 dS = 0.0095 3 (Pgra187_DNA2) ... 2 (Pfre186_DNA2) lnL =-1972.711786 0.03025 3.71696 1.10191 t= 0.0302 S= 345.4 N= 1079.6 dN/dS= 1.1019 dN = 0.0103 dS = 0.0094 4 (Phet26_DNA21) ... 1 (Pdel181_DNA2) lnL =-1921.561815 0.01073 3.11375 1.18654 t= 0.0107 S= 342.5 N= 1082.5 dN/dS= 1.1865 dN = 0.0037 dS = 0.0031 4 (Phet26_DNA21) ... 2 (Pfre186_DNA2) lnL =-1927.106138 0.01287 4.25522 1.54964 t= 0.0129 S= 352.0 N= 1073.0 dN/dS= 1.5496 dN = 0.0047 dS = 0.0030 4 (Phet26_DNA21) ... 3 (Pgra187_DNA2) lnL =-1948.501568 0.02179 4.30601 0.45869 t= 0.0218 S= 349.8 N= 1075.2 dN/dS= 0.4587 dN = 0.0056 dS = 0.0123 5 (Pmex37_DNA21) ... 1 (Pdel181_DNA2) lnL =-1920.298777 0.01053 1.55733 99.00000 t= 0.0105 S= 318.9 N= 1106.1 dN/dS= 99.0000 dN = 0.0045 dS = 0.0000 5 (Pmex37_DNA21) ... 2 (Pfre186_DNA2) lnL =-1914.616800 0.00838 0.77696 99.00000 t= 0.0084 S= 296.5 N= 1128.5 dN/dS= 99.0000 dN = 0.0035 dS = 0.0000 5 (Pmex37_DNA21) ... 3 (Pgra187_DNA2) lnL =-1960.971487 0.02594 4.03558 0.91514 t= 0.0259 S= 348.1 N= 1076.9 dN/dS= 0.9151 dN = 0.0085 dS = 0.0092 5 (Pmex37_DNA21) ... 4 (Phet26_DNA21) lnL =-1913.389962 0.00862 6.08298 0.97563 t= 0.0086 S= 362.3 N= 1062.7 dN/dS= 0.9756 dN = 0.0029 dS = 0.0029 6 (Ptre197_DNA2) ... 1 (Pdel181_DNA2) lnL =-1961.098136 0.02585 4.25957 1.53161 t= 0.0258 S= 349.5 N= 1075.5 dN/dS= 1.5316 dN = 0.0094 dS = 0.0061 6 (Ptre197_DNA2) ... 2 (Pfre186_DNA2) lnL =-1965.694050 0.02802 4.83643 1.71212 t= 0.0280 S= 352.8 N= 1072.2 dN/dS= 1.7121 dN = 0.0104 dS = 0.0061 6 (Ptre197_DNA2) ... 3 (Pgra187_DNA2) lnL =-1901.130192 0.00676 4.05781 0.00100 t= 0.0068 S= 345.2 N= 1079.8 dN/dS= 0.0010 dN = 0.0000 dS = 0.0093 6 (Ptre197_DNA2) ... 4 (Phet26_DNA21) lnL =-1941.618065 0.01954 6.78012 0.64571 t= 0.0195 S= 361.6 N= 1063.4 dN/dS= 0.6457 dN = 0.0057 dS = 0.0089 6 (Ptre197_DNA2) ... 5 (Pmex37_DNA21) lnL =-1953.852896 0.02372 5.63419 1.43296 t= 0.0237 S= 357.2 N= 1067.8 dN/dS= 1.4330 dN = 0.0086 dS = 0.0060 7 (WHR1_DNA225) ... 1 (Pdel181_DNA2) lnL =-1936.561781 0.01511 2.61161 0.72506 t= 0.0151 S= 337.6 N= 1087.4 dN/dS= 0.7251 dN = 0.0046 dS = 0.0064 7 (WHR1_DNA225) ... 2 (Pfre186_DNA2) lnL =-1941.975543 0.01725 3.35589 0.90347 t= 0.0172 S= 345.7 N= 1079.3 dN/dS= 0.9035 dN = 0.0056 dS = 0.0062 7 (WHR1_DNA225) ... 3 (Pgra187_DNA2) lnL =-1960.455637 0.02624 3.64066 0.41889 t= 0.0262 S= 345.9 N= 1079.1 dN/dS= 0.4189 dN = 0.0065 dS = 0.0156 7 (WHR1_DNA225) ... 4 (Phet26_DNA21) lnL =-1928.593448 0.01318 1.68562 0.26826 t= 0.0132 S= 322.2 N= 1102.8 dN/dS= 0.2683 dN = 0.0027 dS = 0.0101 7 (WHR1_DNA225) ... 5 (Pmex37_DNA21) lnL =-1928.718524 0.01300 3.82266 0.60956 t= 0.0130 S= 350.1 N= 1074.9 dN/dS= 0.6096 dN = 0.0037 dS = 0.0061 7 (WHR1_DNA225) ... 6 (Ptre197_DNA2) lnL =-1954.005346 0.02397 5.04975 0.54692 t= 0.0240 S= 355.1 N= 1069.9 dN/dS= 0.5469 dN = 0.0066 dS = 0.0121 8 (YALD273_DNA5) ... 1 (Pdel181_DNA2) lnL =-1921.561815 0.01073 3.11377 1.18654 t= 0.0107 S= 342.5 N= 1082.5 dN/dS= 1.1865 dN = 0.0037 dS = 0.0031 8 (YALD273_DNA5) ... 2 (Pfre186_DNA2) lnL =-1927.106138 0.01287 4.25516 1.54964 t= 0.0129 S= 352.0 N= 1073.0 dN/dS= 1.5496 dN = 0.0047 dS = 0.0030 8 (YALD273_DNA5) ... 3 (Pgra187_DNA2) lnL =-1948.501568 0.02179 4.30601 0.45869 t= 0.0218 S= 349.8 N= 1075.2 dN/dS= 0.4587 dN = 0.0056 dS = 0.0123 8 (YALD273_DNA5) ... 4 (Phet26_DNA21) lnL =-1881.846112 0.00001 8.33165 0.18598 t= 0.0000 S= 369.5 N= 1055.5 dN/dS= 0.1860 dN = 0.0000 dS = 0.0000 8 (YALD273_DNA5) ... 5 (Pmex37_DNA21) lnL =-1913.389962 0.00862 6.08296 0.97563 t= 0.0086 S= 362.3 N= 1062.7 dN/dS= 0.9756 dN = 0.0029 dS = 0.0029 8 (YALD273_DNA5) ... 6 (Ptre197_DNA2) lnL =-1941.618065 0.01954 6.78014 0.64571 t= 0.0195 S= 361.6 N= 1063.4 dN/dS= 0.6457 dN = 0.0057 dS = 0.0089 8 (YALD273_DNA5) ... 7 (WHR1_DNA225) lnL =-1928.593448 0.01318 1.68561 0.26826 t= 0.0132 S= 322.2 N= 1102.8 dN/dS= 0.2683 dN = 0.0027 dS = 0.0101 9 (Pop_trich_ch) ... 1 (Pdel181_DNA2) lnL =-1921.561815 0.01073 3.11378 1.18654 t= 0.0107 S= 342.5 N= 1082.5 dN/dS= 1.1865 dN = 0.0037 dS = 0.0031 9 (Pop_trich_ch) ... 2 (Pfre186_DNA2) lnL =-1927.106138 0.01287 4.25517 1.54964 t= 0.0129 S= 352.0 N= 1073.0 dN/dS= 1.5496 dN = 0.0047 dS = 0.0030 9 (Pop_trich_ch) ... 3 (Pgra187_DNA2) lnL =-1948.501568 0.02179 4.30599 0.45869 t= 0.0218 S= 349.8 N= 1075.2 dN/dS= 0.4587 dN = 0.0056 dS = 0.0123 9 (Pop_trich_ch) ... 4 (Phet26_DNA21) lnL =-1881.845859 0.00001 0.40000 0.00100 t= 0.0000 S= 281.0 N= 1144.0 dN/dS= 0.0010 dN = 0.0000 dS = 0.0000 9 (Pop_trich_ch) ... 5 (Pmex37_DNA21) lnL =-1913.389962 0.00862 6.08299 0.97562 t= 0.0086 S= 362.3 N= 1062.7 dN/dS= 0.9756 dN = 0.0029 dS = 0.0029 9 (Pop_trich_ch) ... 6 (Ptre197_DNA2) lnL =-1941.618065 0.01954 6.78013 0.64571 t= 0.0195 S= 361.6 N= 1063.4 dN/dS= 0.6457 dN = 0.0057 dS = 0.0089 9 (Pop_trich_ch) ... 7 (WHR1_DNA225) lnL =-1928.593448 0.01318 1.68561 0.26826 t= 0.0132 S= 322.2 N= 1102.8 dN/dS= 0.2683 dN = 0.0027 dS = 0.0101 9 (Pop_trich_ch) ... 8 (YALD273_DNA5) lnL =-1881.846052 0.00001 0.40000 0.16519 t= 0.0000 S= 281.0 N= 1144.0 dN/dS= 0.1652 dN = 0.0000 dS = 0.0000 Bio-Tools-Phylo-PAML-1.7.3/t/PAML-parser.t0000644000175000017500000004112513316145226020632 0ustar carandraugcarandraug#!/usr/bin/env perl use utf8; use strict; use warnings; use Test::More; use File::Spec; use Bio::Tools::Phylo::PAML; sub test_input_file { return File::Spec->catfile('t', 'data', @_); } my $inpaml = Bio::Tools::Phylo::PAML->new(-file => test_input_file('codeml_parse.mlc')); ok($inpaml); my $result = $inpaml->next_result; ok($result); is($result->model, 'several dN/dS ratios for branches'); like($result->version, qr'3\.12'); my $MLmat = $result->get_MLmatrix; my $NGmat = $result->get_NGmatrix; is($NGmat->[0]->[1]->{'omega'}, 0.2507); is($NGmat->[0]->[1]->{'dN'}, 0.0863); is($NGmat->[0]->[1]->{'dS'}, 0.3443); is($NGmat->[2]->[3]->{'omega'}, 0.2178); is($NGmat->[2]->[3]->{'dN'}, 0.1348); is($NGmat->[2]->[3]->{'dS'}, 0.6187); is($MLmat->[0]->[1]->{'omega'}, 0.19479); is($MLmat->[0]->[1]->{'dN'}, 0.0839); is($MLmat->[0]->[1]->{'dS'}, 0.4309); is($MLmat->[0]->[1]->{'lnL'}, -1508.607268); is($MLmat->[0]->[1]->{'t'}, 0.47825); is($MLmat->[0]->[1]->{'kappa'}, 2.29137); is($MLmat->[2]->[3]->{'omega'}, 0.16114); is($MLmat->[2]->[3]->{'dN'}, 0.1306); is($MLmat->[2]->[3]->{'dS'}, 0.8105); is($MLmat->[2]->[3]->{'lnL'},-1666.440696); is($MLmat->[2]->[3]->{'t'}, 0.85281); is($MLmat->[2]->[3]->{'kappa'}, 2.21652); my @codonposfreq = $result->get_codon_pos_basefreq(); is($codonposfreq[0]->{'A'}, 0.23579); is($codonposfreq[0]->{'T'}, 0.14737); is($codonposfreq[1]->{'C'}, 0.25123); is($codonposfreq[2]->{'G'}, 0.32842); # AAML parsing - Empirical model $inpaml = Bio::Tools::Phylo::PAML->new(-file => test_input_file('aaml.mlc')); ok($inpaml); $result = $inpaml->next_result; ok($result); is($result->model, 'Empirical (wag.dat)'); my @trees = $result->get_trees; is(@trees, 1); is($trees[0]->score, -1042.768973); is((scalar grep { $_->is_Leaf } $trees[0]->get_nodes), $result->get_seqs); my $aadistmat = $result->get_AADistMatrix(); ok($aadistmat); is($aadistmat->get_entry('Cow', 'Horse'), 0.5462); is($aadistmat->get_entry('Baboon', 'Langur'), 0.1077); my %aafreq = %{$result->get_AAFreqs()}; ok(%aafreq); is($aafreq{'Human'}->{'N'}, 0.0769); is($aafreq{'Human'}->{'R'}, 0.1077); my %ratfreqs = %{$result->get_AAFreqs('Rat')}; is($ratfreqs{'R'},0.0923); is($ratfreqs{'F'},0.0154); my %avgfreqs = %{$result->get_AAFreqs('Average')}; is($avgfreqs{'Q'},0.0411); is($result->get_AAFreqs('Average')->{'I'},0.0424); my $patterns = $result->patterns; my @pat = @{$patterns->{'-patterns'}}; is(scalar @pat, 98); is($patterns->{'-ns'}, 6); is($patterns->{'-ls'}, 130); is((sort $result->get_stat_names)[0], 'constant_sites'); is($result->get_stat('constant_sites'), 46); is($result->get_stat('constant_sites_percentage'), 35.38); # AAML parsing - pairwise model $inpaml = Bio::Tools::Phylo::PAML->new(-file => test_input_file('aaml_pairwise.mlc')); ok($inpaml); $result = $inpaml->next_result; ok($result); is($result->model, 'Empirical_F (wag.dat)'); is($result->get_stat('loglikelihood'),-1189.106658); is($result->get_stat('constant_sites'), 170); is($result->get_stat('constant_sites_percentage'), 59.65); is($result->get_AAFreqs('Average')->{'R'},0.0211); is($result->get_AAFreqs('rabbit')->{'L'},0.1228); $aadistmat = $result->get_AADistMatrix(); ok($aadistmat); is($aadistmat->get_entry('rabbit', 'marsupial'), 0.2877); is($aadistmat->get_entry('human', 'goat-cow'), 0.1439); $aadistmat = $result->get_AAMLDistMatrix(); ok($aadistmat); is($aadistmat->get_entry('rabbit', 'marsupial'), 0.3392); is($aadistmat->get_entry('human', 'goat-cow'), 0.1551); my @seqs = $result->get_seqs; is($seqs[0]->display_id, 'human'); # YN00 parsing, pairwise Ka/Ks from Yang & Nielsen 2000 $inpaml = Bio::Tools::Phylo::PAML->new(-file => test_input_file('yn00.mlc')); ok($inpaml); $result = $inpaml->next_result; ok($result); $MLmat = $result->get_MLmatrix; $NGmat = $result->get_NGmatrix; is($NGmat->[0]->[1]->{'omega'}, 0.251); is($NGmat->[0]->[1]->{'dN'}, 0.0863); is($NGmat->[0]->[1]->{'dS'}, 0.3443); is($NGmat->[2]->[3]->{'omega'}, 0.218); is($NGmat->[2]->[3]->{'dN'}, 0.1348); is($NGmat->[2]->[3]->{'dS'}, 0.6187); is($MLmat->[0]->[1]->{'omega'}, 0.1625); is($MLmat->[0]->[1]->{'dN'}, 0.0818); is($MLmat->[0]->[1]->{'dS'}, 0.5031); is($MLmat->[2]->[3]->{'omega'}, 0.1262); is($MLmat->[2]->[3]->{'dN'}, 0.1298); is($MLmat->[2]->[3]->{'dN_SE'}, 0.0149); is($MLmat->[2]->[3]->{'dS'}, 1.0286); is($MLmat->[2]->[3]->{'dS_SE'}, 0.2614); # codeml NSSites parsing $inpaml = Bio::Tools::Phylo::PAML->new (-file => test_input_file('codeml_nssites.mlc')); ok($inpaml); $result = $inpaml->next_result; ok($result); is($result->model, 'One dN/dS ratio dGamma (ncatG=11)'); is($result->version, 'paml 3.13, August 2002'); $NGmat = $result->get_NGmatrix; ok($NGmat); is($NGmat->[0]->[1]->{'omega'}, 0.2782); is($NGmat->[0]->[1]->{'dN'}, 0.0133); is($NGmat->[0]->[1]->{'dS'}, 0.0478); is($NGmat->[1]->[2]->{'omega'}, 1.1055); is($NGmat->[1]->[2]->{'dN'}, 0.0742); is($NGmat->[1]->[2]->{'dS'}, 0.0671); # this is # model num description # kappa log-likelihood tree length time used # shape alpha/gamma r f my @tstr = ([qw(0 one-ratio 0 4.54006 -906.017440 0.55764 )], [qw(1 neutral 2 4.29790 -902.503869 0.56529 )], [qw(2 selection 3 5.12250 -900.076500 0.6032 )], ); my $iter = 0; my $lastmodel; foreach my $model ( $result->get_NSSite_results ) { my $i = 0; my $r = shift @tstr; is($model->model_num, $r->[$i++]); like($model->model_description, qr/$r->[$i++]/); is($model->num_site_classes,$r->[$i++]); my $tree = $model->next_tree; is($model->kappa, $r->[$i++]); is($model->likelihood,$r->[$i]); is($tree->score, $r->[$i++]); is($tree->total_branch_length, $r->[$i++]); if( $iter == 0 ) { my $params = $model->shape_params; is($params->{'shape'}, 'alpha'); is($params->{'gamma'}, '0.50000'); is($params->{'r'}->[0], '1.00000'); is($params->{'f'}->[0], '1.00000'); } elsif( $iter == 2 ) { my $class = $model->dnds_site_classes; is($class->{'p'}->[0], '0.38160'); is($class->{'w'}->[1], '1.00000'); } $iter++; $lastmodel = $model; } my ($firstsite) = $lastmodel->get_pos_selected_sites; is($firstsite->[0], 15); is($firstsite->[1], 'L'); is($firstsite->[2], 0.6588); # codeml NSSites parsing # for M0 model my $codeml_m0 = Bio::Tools::Phylo::PAML->new (-file => test_input_file('M0.mlc')); ok($codeml_m0); my $result_m0 = $codeml_m0->next_result; my ($nssite_m0,$nssite_m1) = $result_m0->get_NSSite_results; is($nssite_m0->num_site_classes,1); my $class_m0 = $nssite_m0->dnds_site_classes; is($class_m0->{q/p/}->[0],q/1.00000/); is($class_m0->{q/w/}->[0],0.09213); is($nssite_m0->model_num, "0"); @trees= $nssite_m0->get_trees; is (@trees , 1 ); # model 0 is($trees[0]->score, -30.819156); is($nssite_m1->model_num, "1"); @trees= $nssite_m1->get_trees; is($trees[0]->score, -30.819157); # test BASEML # pairwise first my $baseml_p = Bio::Tools::Phylo::PAML->new (-file => test_input_file('baseml.pairwise')); ok($baseml_p); my $baseml = $baseml_p->next_result; my @b_seqs = $baseml->get_seqs; is($b_seqs[0]->seq, 'GTAGAGTACTTT'); is($b_seqs[1]->seq, 'GTAAGAGACGAT'); my @otus = map { $_->display_id } @b_seqs; is(scalar @otus, 3); my $ntfreq = $baseml->get_NTFreqs; ok($ntfreq); is($ntfreq->{$otus[0]}->{'A'}, '0.3333'); is($ntfreq->{$otus[1]}->{'G'}, '0.2105'); my $kappaM = $baseml->get_KappaMatrix; ok($kappaM); is($kappaM->get_entry($otus[1],$otus[0]), '0.3240'); is($kappaM->get_entry($otus[0],$otus[1]), $kappaM->get_entry($otus[1],$otus[0])); is($kappaM->get_entry($otus[1],$otus[2]), '0.1343'); my $alphaM = $baseml->get_AlphaMatrix; ok($alphaM); is($alphaM->get_entry($otus[1],$otus[0]), '9.3595'); is($alphaM->get_entry($otus[0],$otus[1]), $alphaM->get_entry($otus[1],$otus[0])); is($alphaM->get_entry($otus[1],$otus[2]), '1.1101'); is($alphaM->get_entry($otus[0],$otus[2]), '33.1197'); # codeml NSSites parsing # for only 1 model my $codeml_single = Bio::Tools::Phylo::PAML->new (-file => test_input_file('singleNSsite.mlc')); ok($codeml_single); my $result_single = $codeml_single->next_result; my ($nssite_single) = $result_single->get_NSSite_results; is($nssite_single->num_site_classes,q/3/); is($nssite_single->kappa, q/5.28487/); is($nssite_single->likelihood,q/-30.819156/); is($baseml->get_stat('loglikelihood'),-110.532715); is($baseml->get_stat('constant_sites'),46); is($baseml->get_stat('constant_sites_percentage'),'80.70'); is($baseml->model,'HKY85 dGamma (ncatG=5)'); # user trees $baseml_p = Bio::Tools::Phylo::PAML->new (-file => test_input_file('baseml.usertree')); $baseml = $baseml_p->next_result; @trees = $baseml->get_trees; is(@trees, 1); is($trees[0]->score, -129.328757); # codeml NSSites parsing # for branch site model/clade model my $codeml_bs = Bio::Tools::Phylo::PAML->new (-file => test_input_file('branchSite.mlc')); ok($codeml_bs); my $result_bs = $codeml_bs->next_result; my ($nssite_bs) = $result_bs->get_NSSite_results; is($nssite_bs->num_site_classes,q/4/); my $class_bs = $nssite_bs->dnds_site_classes; is($class_bs->{q/p/}->[1],q/0.65968/); is($class_bs->{q/w/}->[1]->{q/background/},q/0.00000/); is($class_bs->{q/w/}->[2]->{q/foreground/},q/999.00000/); # Let's parse the RST file my $paml = Bio::Tools::Phylo::PAML->new (-file => test_input_file('codeml_lysozyme', 'mlc'), -dir => test_input_file('codeml_lysozyme')); $result = $paml->next_result; my ($rst) = grep {$_->id eq 'node#8'} $result->get_rst_seqs; ok($rst); is($rst->seq, join('',qw( AAGGTCTTTGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAGATTGGGACTGGATGGCTAC AGGGGAATCAGCCTAGCAAACTGGATGTGTTTGGCCAAATGGGAGAGTGATTATAACACA CGAGCTACAAACTACAATCCTGGAGACCAAAGCACTGATTATGGGATATTTCAGATCAAT AGCCACTACTGGTGTAATAATGGCAAAACCCCAGGAGCAGTTAATGCCTGTCATATATCC TGCAATGCTTTGCTGCAAGATAACATCGCTGATGCTGTAGCTTGTGCAAAGAGGGTTGTC CGTGATCCACAAGGCATTAGAGCATGGGTGGCATGGAGAAATCATTGTCAAAACAGAGAT GTCAGTCAGTATGTTCAAGGTTGTGGAGTG)), 'node#8 reconstructed seq'); my ($first_tree) = $result->get_rst_trees; my ($node) = $first_tree->find_node(-id => '5_Mmu_rhesus'); my @changes = $node->get_tag_values('changes'); my ($site) = grep { $_->{'site'} == 94 } @changes; is($site->{'anc_aa'}, 'A','ancestral AA'); is($site->{'anc_prob'}, '0.947','ancestral AA'); is($site->{'derived_aa'}, 'T','derived AA'); ($node) = $first_tree->find_node(-id => '12'); @changes = $node->get_tag_values('changes'); ($site) = grep { $_->{'site'} == 88 } @changes; is($site->{'anc_aa'}, 'N','ancestral AA'); is($site->{'anc_prob'}, '0.993','ancestral AA'); is($site->{'derived_aa'}, 'D','derived AA'); is($site->{'derived_prob'}, '0.998','derived AA'); my $persite = $result->get_rst_persite; # minus 1 because we have shifted so that array index matches site number # there are 130 sites in this seq file is(scalar @$persite -1, $result->patterns->{'-ls'}); # let's score site 1 $site = $persite->[2]; # so site 2, node 2 (extant) is($site->[2]->{'codon'}, 'GTC'); is($site->[2]->{'aa'}, 'V'); # site 2, node 3 is($site->[3]->{'codon'}, 'ATC'); is($site->[3]->{'aa'}, 'I'); # ancestral node 9 is($site->[9]->{'codon'}, 'GTC'); is($site->[9]->{'aa'}, 'V'); is($site->[9]->{'prob'}, '1.000'); is($site->[9]->{'Yang95_aa'},'V'); is($site->[9]->{'Yang95_aa_prob'},'1.000'); # ancestral node 10 is($site->[10]->{'codon'}, 'ATC'); is($site->[10]->{'aa'}, 'I'); is($site->[10]->{'prob'}, '0.992'); is($site->[10]->{'Yang95_aa'},'I'); is($site->[10]->{'Yang95_aa_prob'},'0.992'); ## PAML 3.15 my $paml315 = Bio::Tools::Phylo::PAML->new(-file => test_input_file('codeml315.mlc')); $result = $paml315->next_result; is($result->model, 'One dN/dS ratio'); like($result->version, qr'3\.15'); $MLmat = $result->get_MLmatrix; $NGmat = $result->get_NGmatrix; is($NGmat->[0]->[1]->{'omega'}, 0.2264); is($NGmat->[0]->[1]->{'dN'}, 0.0186); is($NGmat->[0]->[1]->{'dS'}, 0.0821); is($MLmat->[0]->[1]->{'omega'}, 0.32693); is($MLmat->[0]->[1]->{'dN'}, '0.0210'); is($MLmat->[0]->[1]->{'dS'}, 0.0644); ## PAML 4 my $codeml4 = Bio::Tools::Phylo::PAML->new(-file => test_input_file('codeml4.mlc')); $result = $codeml4->next_result; is($result->model, 'One dN/dS ratio'); like($result->version, qr'4'); $MLmat = $result->get_MLmatrix; $NGmat = $result->get_NGmatrix; is($NGmat->[0]->[1]->{'omega'}, 0.2507); is($NGmat->[0]->[1]->{'dN'}, 0.0863); is($NGmat->[0]->[1]->{'dS'}, 0.3443); is($MLmat->[0]->[1]->{'omega'}, 0.29075); is($MLmat->[0]->[1]->{'dN'}, '0.0874'); is($MLmat->[0]->[1]->{'dS'}, 0.3006); is($MLmat->[0]->[1]->{'lnL'}, -1596.739984); ## PAML 4.3a # codeml pairwise ML comparison (runmode=-2) my $codeml43 = Bio::Tools::Phylo::PAML->new(-file => test_input_file('codeml43.mlc')); $result = $codeml43->next_result; is($result->model, 'One dN/dS ratio for branches'); like($result->version, qr'4\.3', 'codeml 4.3 runmode=-2'); $MLmat = $result->get_MLmatrix; $NGmat = $result->get_NGmatrix; is($NGmat->[0]->[2]->{'omega'}, 0.2627); is($NGmat->[0]->[2]->{'dN'}, 0.0867); is($NGmat->[0]->[2]->{'dS'}, 0.3301); is($MLmat->[0]->[2]->{'omega'}, 0.19819); is($MLmat->[0]->[2]->{'dN'}, '0.0842'); is($MLmat->[0]->[2]->{'dS'}, 0.4247); is($MLmat->[0]->[2]->{'lnL'}, -1512.583367); ## PAML 4.3a # codeml NSSites parsing (two NSSites models, 1 and 2) { my $codeml43_nssites = Bio::Tools::Phylo::PAML->new (-file => test_input_file('codeml43_nssites.mlc')); ok($codeml43_nssites); my $result = $codeml43_nssites->next_result; ok($result); is($result->model, 'One dN/dS ratio for branches'); like($result->version, qr'4\.3', 'codeml 4.3 two NSSites models'); my $NGmat = $result->get_NGmatrix; ok($NGmat); is($NGmat->[0]->[1]->{'omega'}, 0.2507); is($NGmat->[0]->[1]->{'dN'}, 0.0863); is($NGmat->[0]->[1]->{'dS'}, 0.3443); is($NGmat->[1]->[2]->{'omega'}, 0.2943); is($NGmat->[1]->[2]->{'dN'}, 0.1054); is($NGmat->[1]->[2]->{'dS'}, 0.3581); # these are # "model num" description "number of site classes" kappa log-likelihood "tree length" "time used" my @tstr = ([qw(1 NearlyNeutral 2 2.06684 -2970.527521 2.898 0:08)], [qw(2 PositiveSelection 3 2.18136 -2965.809712 3.589 0:26)],); my $iter = 0; my $lastmodel; foreach my $model ( $result->get_NSSite_results ) { my $i = 0; my $r = shift @tstr; is($model->model_num, $r->[$i++]); like($model->model_description, qr/$r->[$i++]/); is($model->num_site_classes,$r->[$i++]); my $tree = $model->next_tree; is($model->kappa, $r->[$i++]); is($model->likelihood,$r->[$i]); is($tree->score, $r->[$i++]); like($tree->total_branch_length, qr/$r->[$i++]/); if( $iter == 1 ) { my $class = $model->dnds_site_classes; is($class->{'p'}->[0], '0.83347'); is($class->{'w'}->[1], '1.00000'); } $iter++; $lastmodel = $model; } my @sites = $lastmodel->get_NEB_pos_selected_sites; my $firstsite = $sites[0]; my $lastsite = $sites[-1]; is($firstsite->[0], 35, 'NEB positively selected sites'); is($firstsite->[1], 'S'); is($firstsite->[2], 0.643); is($firstsite->[4], '4.400'); is( $lastsite->[0], 264); is( $lastsite->[1], 'P'); is( $lastsite->[2], 0.971); is( $lastsite->[3], '*'); is( $lastsite->[4], 6.134); } # bug #3040 { my $parser = Bio::Tools::Phylo::PAML->new (-file => test_input_file('codeml_nan.mlc')); ok($parser); my $result = $parser->next_result; ok($result); my $MLmatrix = $result->get_MLmatrix(); ok($MLmatrix); is($MLmatrix->[1]->[2]->{'dS'}, 'nan', 'bug 3040'); } # bugs 3365, 3366 { my $parser = Bio::Tools::Phylo::PAML->new (-file => test_input_file('codeml45.mlc')); my $result = $parser->next_result; my @otus = $result->get_seqs(); is(scalar @otus, 9, 'bug 3365'); my $MLmatrix = $result->get_MLmatrix(); is($MLmatrix->[1]->[2]->{dN},0.0103,'bug 3366'); } # bug 3367 { my $parser = Bio::Tools::Phylo::PAML->new (-file => test_input_file('yn00_45.mlc')); my $result = $parser->next_result; my @otus = $result->get_seqs(); is(scalar @otus, 9, 'bug 3367'); } # bug 3332 { my $parser = Bio::Tools::Phylo::PAML->new (-file => test_input_file('codeml45b.mlc')); my $result = $parser->next_result; my $omega2 = $result->get_NGmatrix()->[0]->[1]->{'omega'}; is($result->get_NGmatrix()->[0]->[1]->{'omega'}, '-1.0300', 'bug 3332'); } # bug 3331 { my $parser = Bio::Tools::Phylo::PAML->new (-file => test_input_file('bug3331.mlc')); my $result = $parser->next_result; my $MLmatrix = $result->get_MLmatrix(); my $kappa = $MLmatrix->[0]->[1]->{'kappa'}; is ($kappa, '2.000', 'bug 3331'); } done_testing(); Bio-Tools-Phylo-PAML-1.7.3/t/author-eol.t0000644000175000017500000000164413316145226020670 0ustar carandraugcarandraug BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } use strict; use warnings; # this test was generated with Dist::Zilla::Plugin::Test::EOL 0.19 use Test::More 0.88; use Test::EOL; my @files 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Changes LICENSE MANIFEST META.json META.yml Makefile.PL bin/bp_pairwise_kaks dist.ini lib/Bio/Tools/Phylo/PAML.pm lib/Bio/Tools/Phylo/PAML/Codeml.pm lib/Bio/Tools/Phylo/PAML/ModelResult.pm lib/Bio/Tools/Phylo/PAML/Result.pm lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm t/00-compile.t t/PAML-parser.t t/PAML-run.t t/author-eol.t t/author-mojibake.t t/author-no-tabs.t t/author-pod-coverage.t t/author-pod-syntax.t t/data/M0.mlc t/data/aaml.mlc t/data/aaml_pairwise.mlc t/data/baseml.pairwise t/data/baseml.usertree t/data/branchSite.mlc t/data/bug3331.mlc t/data/codeml.mlc t/data/codeml315.mlc t/data/codeml4.mlc t/data/codeml43.mlc t/data/codeml43_nssites.mlc t/data/codeml45.mlc t/data/codeml45b.mlc t/data/codeml_lysozyme/2NG.dN t/data/codeml_lysozyme/2NG.dS t/data/codeml_lysozyme/2NG.tt t/data/codeml_lysozyme/4fold.nuc t/data/codeml_lysozyme/lnf t/data/codeml_lysozyme/lysozymeSmall.ctl t/data/codeml_lysozyme/lysozymeSmall.trees t/data/codeml_lysozyme/lysozymeSmall.txt t/data/codeml_lysozyme/mlc t/data/codeml_lysozyme/rst t/data/codeml_lysozyme/rst1 t/data/codeml_lysozyme/rub t/data/codeml_nan.mlc t/data/codeml_nssites.mlc t/data/codeml_parse.mlc t/data/cysprot.msf t/data/cysprot.raxml.tre t/data/gf-s85.phylip t/data/singleNSsite.mlc 't/data/test 2.txt' t/data/yn00.mlc t/data/yn00_45.mlc Bio-Tools-Phylo-PAML-1.7.3/lib/0000755000175000017500000000000013316145226016722 5ustar carandraugcarandraugBio-Tools-Phylo-PAML-1.7.3/lib/Bio/0000755000175000017500000000000013316145226017433 5ustar carandraugcarandraugBio-Tools-Phylo-PAML-1.7.3/lib/Bio/Tools/0000755000175000017500000000000013316145226020533 5ustar carandraugcarandraugBio-Tools-Phylo-PAML-1.7.3/lib/Bio/Tools/Phylo/0000755000175000017500000000000013316145226021626 5ustar carandraugcarandraugBio-Tools-Phylo-PAML-1.7.3/lib/Bio/Tools/Phylo/PAML/0000755000175000017500000000000013316145226022357 5ustar carandraugcarandraugBio-Tools-Phylo-PAML-1.7.3/lib/Bio/Tools/Phylo/PAML/Codeml.pm0000644000175000017500000001770013316145226024125 0ustar carandraugcarandraugpackage Bio::Tools::Phylo::PAML::Codeml; $Bio::Tools::Phylo::PAML::Codeml::VERSION = '1.7.3'; use utf8; use strict; use warnings; use vars qw(@ISA); use Bio::Root::Root; use Bio::Root::IO; use Bio::TreeIO; use IO::String; @ISA = qw(Bio::Root::Root Bio::Root::IO ); # ABSTRACT: Parses output from the PAML program codeml # AUTHOR: Jason Stajich # AUTHOR: Aaron Mackey # OWNER: Jason Stajich # OWNER: Aaron Mackey # LICENSE: Perl_5 sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); $self->_parse_mlc(); return $self; } sub get_trees{ my ($self) = @_; } sub get_statistics { my ($self) = @_; } # parse the mlc file sub _parse_mlc { my ($self) = @_; my %data; while( defined( $_ = $self->_readline) ) { print; # Aaron this is where the parsing should begin # I'll do the Tree objects if you like - # I'd do it by building an IO::String for the # the tree data # or does it make more sense to parse this out of a collection of # files? if( /^TREE/ ) { # ... while( defined($_ = $self->_readline) ) { if( /^\(/) { my $treestr = IO::String->new($_); my $treeio = Bio::TreeIO->new(-fh => $treestr, -format => 'newick'); # this is very tenative here!! push @{$self->{'_trees'}}, $treeio->next_tree; } } } } } 1; __END__ =pod =encoding UTF-8 =head1 NAME Bio::Tools::Phylo::PAML::Codeml - Parses output from the PAML program codeml =head1 VERSION version 1.7.3 =head1 SYNOPSIS #!/usr/bin/perl -Tw use strict; use Bio::Tools::Phylo::PAML::Codeml; # need to specify the output file name (or a fh) (defaults to # -file => "codeml.mlc"); also, optionally, the directory in which # the other result files (rst, 2ML.dS, etc) may be found (defaults # to "./") my $parser = new Bio::Tools::Phylo::PAML::Codeml::Parser (-file => "./results/mlc", -dir => "./results/"); # get the first/next result; a Bio::[...]::Codeml::Result object my $result = $parser->next_result(); # get the sequences used in the analysis; returns Bio::PrimarySeq # objects (OTU = Operational Taxonomic Unit). my @otus = $result->get_seqs(); # codon summary: codon usage of each sequence [ arrayref of { # hashref of counts for each codon } for each sequence and the # overall sum ], and positional nucleotide distribution [ arrayref # of { hashref of frequencies for each nucleotide } for each # sequence and overall frequencies ]. my ($codonusage, $ntdist) = $result->get_codon_summary(); # example manipulations of $codonusage and $ntdist: printf "There were %d '%s' codons in the first seq (%s)\n", $codonusage->[0]->{AAA}, 'AAA', $otus[0]->id(); printf "There were %d '%s' codons used in all the sequences\n", $codonusage->[$#{$codonusage}]->{AAA}, 'AAA'; printf "Nucleotide '%c' was present %g of the time in seq %s\n", 'A', $ntdist->[1]->{A}, $otus[1]->id(); # get Nei & Gojobori dN/dS matrix: my $NGmatrix = $result->get_NGmatrix(); # get ML-estimated dN/dS matrix, if calculated; this corresponds to # the runmode = -2, pairwise comparison usage of codeml my $MLmatrix = $result->get_MLmatrix(); # These matrices are length(@otu) x length(@otu) "strict lower # triangle" 2D-matrices, which means that the diagonal and # everything above it is undefined. Each of the defined cells is a # hashref of estimates for "dN", "dS", "omega" (dN/dS ratio), "t", # "S" and "N". If a ML matrix, "lnL" will also be defined. Any # additional ML parameters estimated by the model will be in an # array ref under "params"; it's up to the user to know which # position corresponds to which parameter (since PAML doesn't label # them, and we can't guess very well yet (a TODO I guess). printf "The omega ratio for sequences %s vs %s was: %g\n", $otus[0]->id, $otus[1]->id, $MLmatrix->[0]->[1]->{omega}; # with a little work, these matrices could also be passed to # Bio::Tools::Run::Phylip::Neighbor, or other similar tree-building # method that accepts a matrix of "distances" (using the LOWTRI # option): my $distmat = [ map { [ map { $$_{omega} } @$_ ] } @$MLmatrix ]; # for runmode's other than -2, get tree topology with estimated # branch lengths; returns a Bio::Tree::TreeI-based tree object with # added PAML parameters at each node my $tree = $result->get_tree(); for my $node ($tree->get_nodes()) { # inspect the tree: the "t" (time) parameter is available via # $node->branch_length(); all other branch-specific parameters # ("omega", "dN", etc.) are available via $node->param('omega'); } # get any general model parameters: kappa (the # transition/transversion ratio), NSsites model parameters ("p0", # "p1", "w0", "w1", etc.), etc. my $params = $result->get_model_params(); printf "M1 params: p0 = %g\tp1 = %g\n", $params->{p0}, $params->{p1}; # for NSsites models, obtain posterior probabilities for membership # in each class for every position; probabilities correspond to # classes w0, w1, ... etc. my @probs = $result->get_posteriors(); # find, say, positively selected sites! if ($params->{w2} > 1) { for (my $i = 0; $i < @probs ; $i++) { if ($probs[$i]->[2] > 0.5) { # assumes model M1: three w's, w0, w1 and w2 (positive selection) printf "position %d: (%g prob, %g omega, %g mean w)\n", $i, $probs[$i]->[2], $params->{w2}, $probs[$i]->[3]; } } } else { print "No positive selection found!\n"; } =head1 DESCRIPTION This module is used to parse the output from the PAML program codeml. You can use the Bio::Tools::Run::Phylo::Phylo::PAML::Codeml module to actually run codeml; this module is only useful to parse the output. =head1 METHODS =head2 new Title : new Usage : my $obj = new Bio::Tools::Phylo::PAML::Codeml(); Function: Builds a new Bio::Tools::Phylo::PAML::Codeml object Returns : Bio::Tools::Phylo::PAML::Codeml Args : =head2 get_trees Title : get_trees Usage : my @trees = $codemlparser->get_trees(); Function: Returns a list of trees (if any) are in the output file Returns : List of L objects Args : none =head2 get_statistics Title : get_statistics Usage : my $data = $codemlparser->get_statistics Function: Retrieves the set of pairwise comparisons Returns : Hash Reference keyed as 'seqname' -> 'seqname' -> 'datatype' Args : none =head1 TODO This module should also be able to handle "codemlsites" batch output... =head1 FEEDBACK =head2 Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bio-tools-phylo-paml/issues =head1 AUTHORS Jason Stajich Aaron Mackey =head1 COPYRIGHT This software is copyright (c) by Jason Stajich , and by Aaron Mackey . This software is available under the same terms as the perl 5 programming language system itself. =cut Bio-Tools-Phylo-PAML-1.7.3/lib/Bio/Tools/Phylo/PAML/ModelResult.pm0000644000175000017500000003677713316145226025200 0ustar carandraugcarandraugpackage Bio::Tools::Phylo::PAML::ModelResult; $Bio::Tools::Phylo::PAML::ModelResult::VERSION = '1.7.3'; use utf8; use strict; use warnings; use base qw(Bio::Root::Root); # ABSTRACT: A container for NSSite Model Result from PAML # AUTHOR: Jason Stajich # OWNER: Jason Stajich # LICENSE: Perl_5 sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($modelnum,$modeldesc,$kappa, $timeused,$trees, $pos_sites,$neb_sites,$beb_sites, $num_site_classes, $shape_params, $dnds_classes, $likelihood) = $self->_rearrange([qw(MODEL_NUM MODEL_DESCRIPTION KAPPA TIME_USED TREES POS_SITES NEB_SITES BEB_SITES NUM_SITE_CLASSES SHAPE_PARAMS DNDS_SITE_CLASSES LIKELIHOOD)], @args); if( $trees ) { if(ref($trees) !~ /ARRAY/i ) { $self->warn("Must provide a valid array reference to initialize trees"); } else { foreach my $t ( @$trees ) { $self->add_tree($t); } } } $self->{'_treeiterator'} = 0; if( $pos_sites ) { if(ref($pos_sites) !~ /ARRAY/i ) { $self->warn("Must provide a valid array reference to initialize pos_sites"); } else { foreach my $s ( @$pos_sites ) { if( ref($s) !~ /ARRAY/i ) { $self->warn("Need an array reference for each entry in the pos_sites object"); next; } $self->add_pos_selected_site(@$s); } } } if( $beb_sites ) { if(ref($beb_sites) !~ /ARRAY/i ) { $self->warn("Must provide a valid array reference to initialize beb_sites"); } else { foreach my $s ( @$beb_sites ) { if( ref($s) !~ /ARRAY/i ) { $self->warn("need an array ref for each entry in the beb_sites object"); next; } $self->add_BEB_pos_selected_site(@$s); } } } if( $neb_sites ) { if(ref($neb_sites) !~ /ARRAY/i ) { $self->warn("Must provide a valid array reference to initialize neb_sites"); } else { foreach my $s ( @$neb_sites ) { if( ref($s) !~ /ARRAY/i ) { $self->warn("need an array ref for each entry in the neb_sites object"); next; } $self->add_NEB_pos_selected_site(@$s); } } } defined $modelnum && $self->model_num($modelnum); defined $modeldesc && $self->model_description($modeldesc); defined $kappa && $self->kappa($kappa); defined $timeused && $self->time_used($timeused); defined $likelihood && $self->likelihood($likelihood); $self->num_site_classes($num_site_classes || 0); if( defined $dnds_classes ) { if( ref($dnds_classes) !~ /HASH/i || ! defined $dnds_classes->{'p'} || ! defined $dnds_classes->{'w'} ) { $self->warn("-dnds_site_classes expects a hashref with keys p and w"); } else { $self->dnds_site_classes($dnds_classes); } } if( defined $shape_params ) { if( ref($shape_params) !~ /HASH/i ) { $self->warn("-shape_params expects a hashref not $shape_params\n"); } else { $self->shape_params($shape_params); } } return $self; } sub model_num { my $self = shift; return $self->{'_num'} = shift if @_; return $self->{'_num'}; } sub model_description{ my $self = shift; return $self->{'_model_description'} = shift if @_; return $self->{'_model_description'}; } sub time_used{ my $self = shift; return $self->{'_time_used'} = shift if @_; return $self->{'_time_used'}; } sub kappa{ my $self = shift; return $self->{'_kappa'} = shift if @_; return $self->{'_kappa'}; } sub num_site_classes{ my $self = shift; return $self->{'_num_site_classes'} = shift if @_; return $self->{'_num_site_classes'}; } sub dnds_site_classes{ my $self = shift; return $self->{'_dnds_site_classes'} = shift if @_; return $self->{'_dnds_site_classes'}; } sub get_pos_selected_sites{ return @{$_[0]->{'_posselsites'} || []}; } sub add_pos_selected_site{ my ($self,$site,$aa,$pvalue,$signif) = @_; push @{$self->{'_posselsites'}}, [ $site,$aa,$pvalue,$signif ]; return scalar @{$self->{'_posselsites'}}; } sub get_NEB_pos_selected_sites{ return @{$_[0]->{'_NEBposselsites'} || []}; } sub add_NEB_pos_selected_site{ my ($self,@args) = @_; push @{$self->{'_NEBposselsites'}}, [ @args ]; return scalar @{$self->{'_NEBposselsites'}}; } sub get_BEB_pos_selected_sites{ return @{$_[0]->{'_BEBposselsites'} || []}; } sub add_BEB_pos_selected_site{ my ($self,@args) = @_; push @{$self->{'_BEBposselsites'}}, [ @args ]; return scalar @{$self->{'_BEBposselsites'}}; } sub next_tree{ my ($self,@args) = @_; return $self->{'_trees'}->[$self->{'_treeiterator'}++] || undef; } sub get_trees{ my ($self) = @_; return @{$self->{'_trees'} || []}; } sub rewind_tree_iterator { shift->{'_treeiterator'} = 0; } sub add_tree{ my ($self,$tree) = @_; if( $tree && ref($tree) && $tree->isa('Bio::Tree::TreeI') ) { push @{$self->{'_trees'}},$tree; } return scalar @{$self->{'_trees'}}; } sub shape_params{ my $self = shift; return $self->{'_shape_params'} = shift if @_; return $self->{'_shape_params'}; } sub likelihood{ my $self = shift; return $self->{'likelihood'} = shift if @_; return $self->{'likelihood'}; } 1; __END__ =pod =encoding UTF-8 =head1 NAME Bio::Tools::Phylo::PAML::ModelResult - A container for NSSite Model Result from PAML =head1 VERSION version 1.7.3 =head1 SYNOPSIS # get a ModelResult from a PAML::Result object use Bio::Tools::Phylo::PAML; my $paml = Bio::Tools::Phylo::PAML->new(-file => 'mlc'); my $result = $paml->next_result; foreach my $model ( $result->get_NSSite_results ) { print $model->model_num, " ", $model->model_description, "\n"; print $model->kappa, "\n"; print $model->run_time, "\n"; # if you are using PAML < 3.15 then only one place for POS sites for my $sites ( $model->get_pos_selected_sites ) { print join("\t",@$sites),"\n"; } # otherwise query NEB and BEB slots for my $sites ( $model->get_NEB_pos_selected_sites ) { print join("\t",@$sites),"\n"; } for my $sites ( $model->get_BEB_pos_selected_sites ) { print join("\t",@$sites),"\n"; } } =head1 METHODS =head2 new Title : new Usage : my $obj = Bio::Tools::Phylo::PAML::ModelResult->new(); Function: Builds a new Bio::Tools::Phylo::PAML::ModelResult object Returns : an instance of Bio::Tools::Phylo::PAML::ModelResult Args : -model_num => model number -model_description => model description -kappa => value of kappa -time_used => amount of time -pos_sites => arrayref of sites under positive selection -neb_sites => arrayref of sites under positive selection (by NEB analysis) -beb_sites => arrayref of sites under positive selection (by BEB analysis) -trees => arrayref of tree(s) data for this model -shape_params => hashref of parameters ('shape' => 'alpha', 'gamma' => $g, 'r' => $r, 'f' => $f ) OR ( 'shape' => 'beta', 'p' => $p, 'q' => $q ) -likelihood => likelihood -num_site_classes => number of site classes -dnds_site_classes => hashref with two keys, 'p' and 'w' which each point to an array, each slot is for a different site class. 'w' is for dN/dS and 'p' is probability =head2 model_num Title : model_num Usage : $obj->model_num($newval) Function: Get/Set the Model number (0,1,2,3...) Returns : value of model_num (a scalar) Args : on set, new value (a scalar or undef, optional) =head2 model_description Title : model_description Usage : $obj->model_description($newval) Function: Get/Set the model description This is something like 'one-ratio', 'neutral', 'selection' Returns : value of description (a scalar) Args : on set, new value (a scalar or undef, optional) =head2 time_used Title : time_used Usage : $obj->time_used($newval) Function: Get/Set the time it took to run this analysis Returns : value of time_used (a scalar) Args : on set, new value (a scalar or undef, optional) =head2 kappa Title : kappa Usage : $obj->kappa($newval) Function: Get/Set kappa (ts/tv) Returns : value of kappa (a scalar) Args : on set, new value (a scalar or undef, optional) =head2 num_site_classes Title : num_site_classes Usage : $obj->num_site_classes($newval) Function: Get/Set the number of site classes for this model Returns : value of num_site_classes (a scalar) Args : on set, new value (a scalar or undef, optional) =head2 dnds_site_classes Title : dnds_site_classes Usage : $obj->dnds_site_classes($newval) Function: Get/Set dN/dS site classes, a hashref with 2 keys, 'p' and 'w' which point to arrays one slot for each site class. Returns : value of dnds_site_classes (a hashref) Args : on set, new value (a scalar or undef, optional) =head2 get_pos_selected_sites Title : get_pos_selected_sites Usage : my @sites = $modelresult->get_pos_selected_sites(); Function: Get the sites which PAML has identified as under positive selection (w > 1). This returns an array with each slot being a site, 4 values, site location (in the original alignment) Amino acid (I *think* in the first sequence) P (P value) Significance (** indicated > 99%, * indicates >=95%) Returns : Array Args : none =head2 add_pos_selected_site Title : add_pos_selected_site Usage : $result->add_pos_selected_site($site,$aa,$pvalue,$signif); Function: Add a site to the list of positively selected sites Returns : count of the number of sites stored Args : $site - site number (in the alignment) $aa - amino acid under selection $pvalue - float from 0->1 represent probability site is under selection according to this model $signif - significance (coded as either empty, '*', or '**' =head2 get_NEB_pos_selected_sites Title : get_NEB_pos_selected_sites Usage : my @sites = $modelresult->get_NEB_pos_selected_sites(); Function: Get the sites which PAML has identified as under positive selection (w > 1) using Naive Empirical Bayes. This returns an array with each slot being a site, 4 values, site location (in the original alignment) Amino acid (I *think* in the first sequence) P (P value) Significance (** indicated > 99%, * indicates > 95%) post mean for w Returns : Array Args : none =head2 add_NEB_pos_selected_site Title : add_NEB_pos_selected_site Usage : $result->add_NEB_pos_selected_site($site,$aa,$pvalue,$signif); Function: Add a site to the list of positively selected sites Returns : count of the number of sites stored Args : $site - site number (in the alignment) $aa - amino acid under selection $pvalue - float from 0->1 represent probability site is under selection according to this model $signif - significance (coded as either empty, '*', or '**' $postmean - post mean for w =head2 get_BEB_pos_selected_sites Title : get_BEB_pos_selected_sites Usage : my @sites = $modelresult->get_BEB_pos_selected_sites(); Function: Get the sites which PAML has identified as under positive selection (w > 1) using Bayes Empirical Bayes. This returns an array with each slot being a site, 6 values, site location (in the original alignment) Amino acid (I *think* in the first sequence) P (P value) Significance (** indicated > 99%, * indicates > 95%) post mean for w (mean) Standard Error for w (SE) Returns : Array Args : none =head2 add_BEB_pos_selected_site Title : add_BEB_pos_selected_site Usage : $result->add_BEB_pos_selected_site($site,$aa,$pvalue,$signif); Function: Add a site to the list of positively selected sites Returns : count of the number of sites stored Args : $site - site number (in the alignment) $aa - amino acid under selection $pvalue - float from 0->1 represent probability site is under selection according to this model $signif - significance (coded as either empty, '*', or '**' $postmean - post mean for w $SE - Standard Error for w =head2 next_tree Title : next_tree Usage : my $tree = $factory->next_tree; Function: Get the next tree from the factory Returns : L Args : none =head2 get_trees Title : get_trees Usage : my @trees = $result->get_trees; Function: Get all the parsed trees as an array Returns : Array of trees Args : none =head2 rewind_tree_iterator Title : rewind_tree_iterator Usage : $result->rewind_tree_iterator() Function: Rewinds the tree iterator so that next_tree can be called again from the beginning Returns : none Args : none =head2 add_tree Title : add_tree Usage : $result->add_tree($tree); Function: Adds a tree Returns : integer which is the number of trees stored Args : L =head2 shape_params Title : shape_params Usage : $obj->shape_params($newval) Function: Get/Set shape params for the distribution, 'alpha', 'beta' which is a hashref with 1 keys, 'p' and 'q' Returns : value of shape_params (a scalar) Args : on set, new value (a scalar or undef, optional) =head2 likelihood Title : likelihood Usage : $obj->likelihood($newval) Function: log likelihood Returns : value of likelihood (a scalar) Args : on set, new value (a scalar or undef, optional) =head1 FEEDBACK =head2 Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bio-tools-phylo-paml/issues =head1 AUTHOR Jason Stajich =head1 COPYRIGHT This software is copyright (c) by Jason Stajich . This software is available under the same terms as the perl 5 programming language system itself. =cut Bio-Tools-Phylo-PAML-1.7.3/lib/Bio/Tools/Phylo/PAML/Result.pm0000644000175000017500000006726613316145226024214 0ustar carandraugcarandraugpackage Bio::Tools::Phylo::PAML::Result; $Bio::Tools::Phylo::PAML::Result::VERSION = '1.7.3'; use utf8; use strict; use warnings; use base qw(Bio::Root::Root Bio::AnalysisResultI); # ABSTRACT: A PAML result set object # AUTHOR: Jason Stajich # AUTHOR: Aaron Mackey # OWNER: Jason Stajich # OWNER: Aaron Mackey # LICENSE: Perl_5 # AUTHOR: Albert Vilella sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($trees,$mlmat,$seqs,$ngmatrix, $codonpos,$codonfreq,$version, $model,$patterns, $stats, $aafreq, $aadistmat, $aamldistmat, $ntfreqs, $seqfile, $kappa_mat, $alpha_mat, $NSSitesresults,$input_params,$rst,$rst_persite,$rst_trees ) = $self->_rearrange([qw (TREES MLMATRIX SEQS NGMATRIX CODONPOS CODONFREQ VERSION MODEL PATTERNS STATS AAFREQ AADISTMAT AAMLDISTMAT NTFREQ SEQFILE KAPPA_DISTMAT ALPHA_DISTMAT NSSITESRESULTS INPUT_PARAMS RST RST_PERSITE RST_TREES)], @args); $self->reset_seqs; if( $trees ) { if(ref($trees) !~ /ARRAY/i ) { $self->warn("Must provide a valid array reference to initialize trees"); } else { foreach my $t ( @$trees ) { $self->add_tree($t); } } } $self->{'_treeiterator'} = 0; if( $mlmat ) { if( ref($mlmat) !~ /ARRAY/i ) { $self->warn("Must provide a valid array reference to initialize MLmatrix"); } else { $self->set_MLmatrix($mlmat); } } if( $seqs ) { if( ref($seqs) !~ /ARRAY/i ) { $self->warn("Must provide a valid array reference to initialize seqs"); } else { foreach my $s ( @$seqs ) { $self->add_seq($s); } } } if( $ngmatrix ) { if( ref($ngmatrix) !~ /ARRAY/i ) { $self->warn("Must provide a valid array reference to initialize NGmatrix"); } else { $self->set_NGmatrix($ngmatrix); } } if( $codonfreq ) { if( ref($codonfreq) =~ /ARRAY/i ) { $self->set_CodonFreqs($codonfreq); } else { $self->warn("Must provide a valid array reference to initialize codonfreq"); } } if( $codonpos ) { if( ref($codonpos) !~ /ARRAY/i ) { $self->warn("Must provide a valid array reference to initialize codonpos"); } else { $self->set_codon_pos_basefreq(@$codonpos); } } $self->version($version) if defined $version; $self->seqfile($seqfile) if defined $seqfile; $self->model($model) if defined $model; if( defined $patterns ) { if( ref($patterns) =~ /HASH/i ) { $self->patterns($patterns); } else { $self->warn("Must provide a valid array reference to initialize patterns"); } } $self->{'_aafreqs'} = {}; if( $aafreq ) { if( ref($aafreq) =~ /HASH/i ) { $self->set_AAFreqs($aafreq); } else { $self->warn("Must provide a valid hash reference to initialize aafreq"); } } if( $stats ) { if( ref($stats) =~ /HASH/i ) { while( my ($stat,$val) = each %$stats) { $self->add_stat($stat,$val); } } else { $self->warn("Must provide a valid hash reference initialize stats"); } } $self->set_AADistMatrix($aadistmat) if defined $aadistmat; $self->set_AAMLDistMatrix($aamldistmat) if defined $aamldistmat; if( defined $NSSitesresults ) { if( ref($NSSitesresults) !~ /ARRAY/i ) { $self->warn("expected an arrayref for -NSSitesresults"); } else { foreach my $m ( @$NSSitesresults ) { $self->add_NSSite_result($m); } } } $self->{'_ntfreqs'} = {}; if( $ntfreqs ) { if( ref($ntfreqs) =~ /HASH/i ) { $self->set_NTFreqs($ntfreqs); } else { $self->warn("Must provide a valid hash reference to initialize ntfreq"); } } if( $kappa_mat ) { $self->set_KappaMatrix($kappa_mat); } if( $alpha_mat ) { $self->set_AlphaMatrix($alpha_mat); } if( $input_params ) { if( ref($input_params) !~ /HASH/i ) { $self->warn("Must provide a valid hash object for input_params\n"); } else { while( my ($p,$v) = each %$input_params ) { $self->set_input_parameter($p,$v); } } } $self->reset_rst_seqs; if( $rst ) { if( ref($rst) =~ /ARRAY/i ) { for ( @$rst ) { $self->add_rst_seq($_); } } else { $self->warn("Need a valid array ref for -rst option\n"); } } if( defined $rst_persite ) { $self->set_rst_persite($rst_persite); } $self->reset_rst_trees; if( $rst_trees ) { if( ref($rst_trees) =~ /ARRAY/i ) { for ( @$rst_trees ) { $self->add_rst_tree($_); } } else { $self->warn("Need a valid array ref for -rst_trees option\n"); } } return $self; } sub next_tree{ my ($self,@args) = @_; return $self->{'_trees'}->[$self->{'_treeiterator'}++] || undef; } sub get_trees{ my ($self) = @_; return @{$self->{'_trees'} || []}; } sub rewind_tree_iterator { shift->{'_treeiterator'} = 0; } sub add_tree{ my ($self,$tree) = @_; if( $tree && ref($tree) && $tree->isa('Bio::Tree::TreeI') ) { push @{$self->{'_trees'}},$tree; } return scalar @{$self->{'_trees'}}; } sub set_MLmatrix{ my ($self,$mat) = @_; return unless ( defined $mat ); if( ref($mat) !~ /ARRAY/i ) { $self->warn("Did not provide a valid 2D Array reference for set_MLmatrix"); return; } $self->{'_mlmatrix'} = $mat; } sub get_MLmatrix{ my ($self,@args) = @_; return $self->{'_mlmatrix'}; } sub set_NGmatrix{ my ($self,$mat) = @_; return unless ( defined $mat ); if( ref($mat) !~ /ARRAY/i ) { $self->warn("Did not provide a valid 2D Array reference for set_NGmatrix"); return; } $self->{'_ngmatrix'} = $mat; } sub get_NGmatrix{ my ($self,@args) = @_; return $self->{'_ngmatrix'}; } sub add_seq{ my ($self,$seq) = @_; if( $seq ) { unless( $seq->isa("Bio::PrimarySeqI") ) { $self->warn("Must provide a valid Bio::PrimarySeqI to add_seq"); return; } push @{$self->{'_seqs'}},$seq; } } sub reset_seqs{ my ($self) = @_; $self->{'_seqs'} = []; } sub get_seqs{ my ($self) = @_; return @{$self->{'_seqs'}}; } sub set_codon_pos_basefreq { my ($self,@codonpos) = @_; if( scalar @codonpos != 3 ) { $self->warn("invalid array to set_codon_pos_basefreq, must be an array of length 3"); return; } foreach my $pos ( @codonpos ) { if( ref($pos) !~ /HASH/i || ! exists $pos->{'A'} ) { $self->warn("invalid array to set_codon_pos_basefreq, must be an array with hashreferences keyed on DNA bases, C,A,G,T"); } } $self->{'_codonposbasefreq'} = [@codonpos]; } sub get_codon_pos_basefreq{ my ($self) = @_; return @{$self->{'_codonposbasefreq'}}; } sub version{ my $self = shift; $self->{'_version'} = shift if @_; return $self->{'_version'}; } sub seqfile{ my $self = shift; $self->{'_seqfile'} = shift if @_; return $self->{'_seqfile'}; } sub model{ my $self = shift; return $self->{'_model'} = shift if @_; return $self->{'_model'}; } sub patterns{ my $self = shift; return $self->{'_patterns'} = shift if @_; return $self->{'_patterns'}; } sub set_AAFreqs{ my ($self,$aafreqs) = @_; if( $aafreqs && ref($aafreqs) =~ /HASH/i ) { foreach my $seqname ( keys %{$aafreqs} ) { $self->{'_aafreqs'}->{$seqname} = $aafreqs->{$seqname}; } } } sub get_AAFreqs{ my ($self,$seqname) = @_; if( $seqname ) { return $self->{'_aafreqs'}->{$seqname} || {}; } else { return $self->{'_aafreqs'}; } } sub set_NTFreqs{ my ($self,$freqs) = @_; if( $freqs && ref($freqs) =~ /HASH/i ) { foreach my $seqname ( keys %{$freqs} ) { $self->{'_ntfreqs'}->{$seqname} = $freqs->{$seqname}; } } } sub get_NTFreqs{ my ($self,$seqname) = @_; if( $seqname ) { return $self->{'_ntfreqs'}->{$seqname} || {}; } else { return $self->{'_ntfreqs'}; } } sub add_stat{ my ($self,$stat,$value) = @_; return if( ! defined $stat || !defined $value ); $self->{'_stats'}->{$stat} = $value; return; } sub get_stat{ my ($self,$statname) = @_; return $self->{'_stats'}->{$statname}; } sub get_stat_names{ my ($self) = @_; return keys %{$self->{'_stats'} || {}}; } sub get_AADistMatrix{ my $self = shift; return $self->{'_AADistMatix'}; } sub set_AADistMatrix{ my ($self,$d) = @_; if( ! $d || ! ref($d) || ! $d->isa('Bio::Matrix::PhylipDist') ) { $self->warn("Must provide a valid Bio::Matrix::MatrixI for set_AADistMatrix"); } $self->{'_AADistMatix'} = $d; return; } sub get_AAMLDistMatrix{ my $self = shift; return $self->{'_AAMLDistMatix'}; } sub set_AAMLDistMatrix{ my ($self,$d) = @_; if( ! $d || ! ref($d) || ! $d->isa('Bio::Matrix::PhylipDist') ) { $self->warn("Must provide a valid Bio::Matrix::MatrixI for set_AAMLDistMatrix"); } $self->{'_AAMLDistMatix'} = $d; return; } sub add_NSSite_result{ my ($self,$model) = @_; if( defined $model ) { push @{$self->{'_nssiteresult'}}, $model; } return scalar @{$self->{'_nssiteresult'}}; } sub get_NSSite_results{ my ($self) = @_; return @{$self->{'_nssiteresult'} || []}; } sub set_CodonFreqs{ my $self = shift; return $self->{'_codonfreqs'} = shift if @_; return $self->{'_codonfreqs'}; } sub get_CodonFreqs{ my ($self) = @_; return @{$self->{'_codonfreqs'} || []}; } sub get_KappaMatrix{ my $self = shift; return $self->{'_KappaMatix'}; } sub set_KappaMatrix{ my ($self,$d) = @_; if( ! $d || ! ref($d) || ! $d->isa('Bio::Matrix::PhylipDist') ) { $self->warn("Must provide a valid Bio::Matrix::MatrixI for set_NTDistMatrix"); } $self->{'_KappaMatix'} = $d; return; } sub get_AlphaMatrix{ my $self = shift; return $self->{'_AlphaMatix'}; } sub set_AlphaMatrix{ my ($self,$d) = @_; if( ! $d || ! ref($d) || ! $d->isa('Bio::Matrix::PhylipDist') ) { $self->warn("Must provide a valid Bio::Matrix::MatrixI for set_NTDistMatrix"); } $self->{'_AlphaMatix'} = $d; return; } sub set_input_parameter{ my ($self,$p,$v) = @_; return unless defined $p; $self->{'_input_parameters'}->{$p} = $v; } sub get_input_parameters{ my ($self) = @_; return %{$self->{'_input_parameters'} || {}}; } sub reset_input_parameters{ my ($self) = @_; $self->{'_input_parameters'} = {}; } sub add_rst_seq{ my ($self,$seq) = @_; if( $seq ) { unless( $seq->isa("Bio::PrimarySeqI") ) { $self->warn("Must provide a valid Bio::PrimarySeqI to add_rst_seq"); return; } push @{$self->{'_rstseqs'}},$seq; } } sub reset_rst_seqs{ my ($self) = @_; $self->{'_rstseqs'} = []; } sub get_rst_seqs{ my ($self) = @_; return @{$self->{'_rstseqs'} || []}; } sub add_rst_tree{ my ($self,$tree) = @_; if( $tree ) { unless( $tree->isa("Bio::Tree::TreeI") ) { $self->warn("Must provide a valid Bio::Tree::TreeI to add_rst_tree not $tree"); return; } push @{$self->{'_rsttrees'}},$tree; } } sub reset_rst_trees{ my ($self) = @_; $self->{'_rsttrees'} = []; } sub get_rst_trees{ my ($self) = @_; return @{$self->{'_rsttrees'} || []}; } sub set_rst_persite{ my $self = shift; return $self->{'_rstpersite'} = shift if @_; return $self->{'_rstpersite'}; } sub get_rst_persite{ my ($self) = @_; return $self->{'_rstpersite'} || []; } 1; __END__ =pod =encoding UTF-8 =head1 NAME Bio::Tools::Phylo::PAML::Result - A PAML result set object =head1 VERSION version 1.7.3 =head1 SYNOPSIS # see Bio::Tools::Phylo::PAML for example usage use Bio::Tools::Phylo::PAML; my $parser = Bio::Tools::Phylo::PAML->new (-file => "./results/mlc", -dir => "./results/"); # get the first/next result; a Bio::Tools::Phylo::PAML::Result object, # which isa Bio::SeqAnalysisResultI object. my $result = $parser->next_result(); my @seqs = $result->get_seqs; my %input_params = $result->get_input_parameters; my @basfreq = $result->get_codon_pos_basefreq; my $MLmatrix = $result->get_MLmatrix; # get MaxLikelihood Matrix my $NGmatrix = $result->get_NGmatrix; # get Nei-Gojoburi Matrix # for AAML runs my $AAmatrix = $result->get_AADistMatrix; my $AAMLmatrix = $result->get_AAMLDistMatrix; # if -dir contains an rst file get list of # Bio::PrimarySeq ancestral state reconstructions of the sequences my @rsts = $result->get_rst_seqs; # if you want to print the changes on the tree # this will print out the # anc_aa => ANCESTRAL AMINO ACID # anc_prob => ANCESTRAL AA PROBABILITY # derived_aa => DERIVED AA # derived_prob => DERIVE AA PROBABILITY (where appropriate - NA for extant/tip taxas) # site => which codon site this in the alignment @trees = $result->get_rst_trees; for my $t ( @trees ) { for my $node ( $t->get_nodes ) { next unless $node->ancestor; # skip root node my @changes = $node->get_tag_values('changes'); my $chgstr = ''; for my $c ( @changes ) { for my $k ( sort keys %$c ) { $chgstr .= "$k => $c->{$k} "; } $chgstr .= "\n\t"; } printf "node:%s n=%s s=%s\n\t%s\n", $node->id, $node->get_tag_values('n'), $node->get_tag_values('s'), $chgstr; } } # Persite probabilities my $persite = $result->get_rst_persite; # let's score site 1 $site = $persite->[2]; # so site 2, node 2 (extant node, node 2) print $site->[2]->{'codon'}, ' ',$site->[2]->{'aa'},"\n"; # site 2, node 3 print $site->[3]->{'codon'}, ' ',$site->[3]->{'aa'}, "\n"; # ancestral node 9, codon, aa, marginal probabilities; Yang95 is listed as # (eqn. 4 in Yang et al. 1995 Genetics 141:1641-1650) in PAML rst file. print $site->[9]->{'codon'}, ' ',$site->[9]->{'aa'}, ' ', $site->[9]->{'prob'}, ' ', $site->[9]->{'Yang95_aa'},' ', $site->[9]->{'Yang95_aa_prob'},"\n"; =head1 DESCRIPTION This is a container object for PAML Results. =head1 METHODS =head2 new Title : new Usage : my $obj = Bio::Tools::Phylo::PAML::Result->new(%data); Function: Builds a new Bio::Tools::Phylo::PAML::Result object Returns : Bio::Tools::Phylo::PAML::Result Args : -trees => array reference of Bio::Tree::TreeI objects -MLmatrix => ML matrix -seqs => array reference of Bio::PrimarySeqI objects -codonpos => array reference of codon positions -codonfreq => array reference of codon frequencies -version => version string -model => model string -patterns => hashref with the fields '-patterns', '-ns', '-ls' -stats => array ref of misc stats (optional) -aafreq => Hashref of AA frequencies (only for AAML) -aadistmat => Bio::Matrix::PhylipDist (only for AAML) -aamldistmat => Bio::Matrix::PhylipDist (only for pairwise AAML) -ntfreq => array ref of NT frequencies (only for BASEML) -seqfile => seqfile used -kappa_mat => Bio::Matrix::PhylipDist of kappa values (only for BASEML) -alpha_mat => Bio::Matrix::PhylipDist of alpha values (only for BASEML) -NSSitesresult => arrayref of PAML::ModelResult -input_params => input params from .ctl file -rst => array reference of Bio::PrimarySeqI objects of ancestral state reconstruction -rst_persite=> arrayref of persite data, this is a complicated set of AoH -rst_trees => rst trees with changes coded on the tree See Also: L, L, L, L =head2 next_tree Title : next_tree Usage : my $tree = $factory->next_tree; Function: Get the next tree from the factory Returns : L Args : none =head2 get_trees Title : get_trees Usage : my @trees = $result->get_trees; Function: Get all the parsed trees as an array Returns : Array of trees Args : none =head2 rewind_tree_iterator Title : rewind_tree_iterator Usage : $result->rewind_tree_iterator() Function: Rewinds the tree iterator so that next_tree can be called again from the beginning Returns : none Args : none =head2 add_tree Title : add_tree Usage : $result->add_tree($tree); Function: Adds a tree Returns : integer which is the number of trees stored Args : L =head2 set_MLmatrix Title : set_MLmatrix Usage : $result->set_MLmatrix($mat) Function: Set the ML Matrix Returns : none Args : Arrayref to MLmatrix (must be arrayref to 2D matrix whic is lower triangle pairwise) =head2 get_MLmatrix Title : get_MLmatrix Usage : my $mat = $result->get_MLmatrix() Function: Get the ML matrix Returns : 2D Array reference Args : none =head2 set_NGmatrix Title : set_NGmatrix Usage : $result->set_NGmatrix($mat) Function: Set the Nei & Gojobori Matrix Returns : none Args : Arrayref to NGmatrix (must be arrayref to 2D matrix whic is lower triangle pairwise) =head2 get_NGmatrix Title : get_NGmatrix Usage : my $mat = $result->get_NGmatrix() Function: Get the Nei & Gojobori matrix Returns : 2D Array reference Args : none =head2 add_seq Title : add_seq Usage : $obj->add_seq($seq) Function: Add a Bio::PrimarySeq to the Result Returns : none Args : Bio::PrimarySeqI See also : L =head2 reset_seqs Title : reset_seqs Usage : $result->reset_seqs Function: Reset the OTU seqs stored Returns : none Args : none =head2 get_seqs Title : get_seqs Usage : my @otus = $result->get_seqs Function: Get the seqs Bio::PrimarySeq (OTU = Operational Taxonomic Unit) Returns : Array of Bio::PrimarySeq Args : None See also : L =head2 set_codon_pos_basefreq Title : set_codon_pos_basefreq Usage : $result->set_codon_pos_basefreq(@freqs) Function: Set the codon position base frequencies Returns : none Args : Array of length 3 where each slot has a hashref keyed on DNA base =head2 get_codon_pos_basefreq Title : get_codon_pos_basefreq Usage : my @basepos = $result->get_codon_pos_basefreq; Function: Get the codon position base frequencies Returns : Array of length 3 (each codon position), each slot is a hashref keyed on DNA bases, the values are the frequency of the base at that position for all sequences Args : none Note : The array starts at 0 so position '1' is in position '0' of the array =head2 version Title : version Usage : $obj->version($newval) Function: Get/Set version Returns : value of version Args : newvalue (optional) =head2 seqfile Title : seqfile Usage : $obj->seqfile($newval) Function: Get/Set seqfile Returns : value of seqfile Args : newvalue (optional) =head2 model Title : model Usage : $obj->model($newval) Function: Get/Set model Returns : value of model Args : on set, new value (a scalar or undef, optional) =head2 patterns Title : patterns Usage : $obj->patterns($newval) Function: Get/Set Patterns hash Returns : Hashref of pattern data Args : [optional] Hashref of patterns : The hashref is typically : { -patterns => \@arrayref : -ns => $ns : -ls => $ls : } =head2 set_AAFreqs Title : set_AAFreqs Usage : $result->set_AAFreqs(\%aafreqs); Function: Get/Set AA freqs Returns : none Args : Hashref, keys are the sequence names, each points to a hashref which in turn has keys which are the amino acids =head2 get_AAFreqs Title : get_AAFreqs Usage : my %all_aa_freqs = $result->get_AAFreqs() OR my %seq_aa_freqs = $result->get_AAFreqs($seqname) Function: Get the AA freqs, either for every sequence or just for a specific sequence The average aa freqs for the entire set are also available for the sequence named 'Average' Returns : Hashref Args : (optional) sequence name to retrieve aa freqs for =head2 set_NTFreqs Title : set_NTFreqs Usage : $result->set_NTFreqs(\%aafreqs); Function: Get/Set NT freqs Returns : none Args : Hashref, keys are the sequence names, each points to a hashref which in turn has keys which are the amino acids =head2 get_NTFreqs Title : get_NTFreqs Usage : my %all_nt_freqs = $result->get_NTFreqs() OR my %seq_nt_freqs = $result->get_NTFreqs($seqname) Function: Get the NT freqs, either for every sequence or just for a specific sequence The average nt freqs for the entire set are also available for the sequence named 'Average' Returns : Hashref Args : (optional) sequence name to retrieve nt freqs for =head2 add_stat Title : add_stat Usage : $result->add_stat($stat,$value); Function: Add some misc stat valuess (key/value pairs) Returns : none Args : $stat stat name $value stat value =head2 get_stat Title : get_stat Usage : my $value = $result->get_stat($name); Function: Get the value for a stat of a given name Returns : scalar value Args : name of the stat =head2 get_stat_names Title : get_stat_names Usage : my @names = $result->get_stat_names; Function: Get the stat names stored for the result Returns : array of names Args : none =head2 get_AADistMatrix Title : get_AADistMatrix Usage : my $mat = $obj->get_AADistMatrix() Function: Get AADistance Matrix Returns : value of AADistMatrix (Bio::Matrix::PhylipDist) Args : none =head2 set_AADistMatrix Title : set_AADistMatrix Usage : $obj->set_AADistMatrix($mat); Function: Set the AADistrance Matrix (Bio::Matrix::PhylipDist) Returns : none Args : AADistrance Matrix (Bio::Matrix::PhylipDist) =head2 get_AAMLDistMatrix Title : get_AAMLDistMatrix Usage : my $mat = $obj->get_AAMLDistMatrix() Function: Get AAMLDistance Matrix Returns : value of AAMLDistMatrix (Bio::Matrix::PhylipDist) Args : none =head2 set_AAMLDistMatrix Title : set_AAMLDistMatrix Usage : $obj->set_AAMLDistMatrix($mat); Function: Set the AA ML Distrance Matrix (Bio::Matrix::PhylipDist) Returns : none Args : AAMLDistrance Matrix (Bio::Matrix::PhylipDist) =head2 add_NSSite_result Title : add_NSSite_result Usage : $result->add_NSSite_result($model) Function: Add a NSsite result (PAML::ModelResult) Returns : none Args : Bio::Tools::Phylo::PAML::ModelResult =head2 get_NSSite_results Title : get_NSSite_results Usage : my @results = @{$self->get_NSSite_results}; Function: Get the reference to the array of NSSite_results Returns : Array of PAML::ModelResult results Args : none =head2 set_CodonFreqs Title : set_CodonFreqs Usage : $obj->set_CodonFreqs($newval) Function: Get/Set the Codon Frequence table Returns : value of set_CodonFreqs (a scalar) Args : on set, new value (a scalar or undef, optional) =head2 get_CodonFreqs Title : get_CodonFreqs Usage : my @codon_freqs = $result->get_CodonFreqs() Function: Get the Codon freqs Returns : Array Args : none =head2 get_KappaMatrix Title : get_KappaMatrix Usage : my $mat = $obj->get_KappaMatrix() Function: Get KappaDistance Matrix Returns : value of KappaMatrix (Bio::Matrix::PhylipDist) Args : none =head2 set_KappaMatrix Title : set_KappaMatrix Usage : $obj->set_KappaMatrix($mat); Function: Set the KappaDistrance Matrix (Bio::Matrix::PhylipDist) Returns : none Args : KappaDistrance Matrix (Bio::Matrix::PhylipDist) =head2 get_AlphaMatrix Title : get_AlphaMatrix Usage : my $mat = $obj->get_AlphaMatrix() Function: Get AlphaDistance Matrix Returns : value of AlphaMatrix (Bio::Matrix::PhylipDist) Args : none =head2 set_AlphaMatrix Title : set_AlphaMatrix Usage : $obj->set_AlphaMatrix($mat); Function: Set the AlphaDistrance Matrix (Bio::Matrix::PhylipDist) Returns : none Args : AlphaDistrance Matrix (Bio::Matrix::PhylipDist) =head2 set_input_parameter Title : set_input_parameter Usage : $obj->set_input_parameter($p,$vl); Function: Set an Input Parameter Returns : none Args : $parameter and $value =head2 get_input_parameters Title : get_input_parameters Usage : $obj->get_input_parameters; Function: Get Input Parameters Returns : Hash of key/value pairs Args : none =head2 reset_input_parameters Title : reset_input_parameters Usage : $obj->reset_input_parameters; Function: Reset the Input Parameters hash Returns : none Args : none =head2 add_rst_seq Title : add_rst_seq Usage : $obj->add_rst_seq($seq) Function: Add a Bio::PrimarySeq to the RST Result Returns : none Args : Bio::PrimarySeqI See also : L =head2 reset_rst_seqs Title : reset_rst_seqs Usage : $result->reset_rst_seqs Function: Reset the RST seqs stored Returns : none Args : none =head2 get_rst_seqs Title : get_rst_seqs Usage : my @otus = $result->get_rst_seqs Function: Get the seqs Bio::PrimarySeq Returns : Array of Bio::PrimarySeqI objects Args : None See also : L =head2 add_rst_tree Title : add_rst_tree Usage : $obj->add_rst_tree($tree) Function: Add a Bio::Tree::TreeI to the RST Result Returns : none Args : Bio::Tree::TreeI See also : L =head2 reset_rst_trees Title : reset_rst_trees Usage : $result->reset_rst_trees Function: Reset the RST trees stored Returns : none Args : none =head2 get_rst_trees Title : get_rst_trees Usage : my @otus = $result->get_rst_trees Function: Get the trees Bio::Tree::TreeI Returns : Array of Bio::Tree::TreeI objects Args : None See also : L =head2 set_rst_persite Title : set_rst_persite Usage : $obj->set_rst_persite($newval) Function: Get/Set the per-site RST values Returns : value of set_rst_persite (a scalar) Args : on set, new value (a scalar or undef, optional) =head2 get_rst_persite Title : get_rst_persite Usage : my @rst_persite = @{$result->get_rst_persite()} Function: Get the per-site RST values Returns : Array Args : none =head1 Reconstructed Ancestral State relevant options =head1 FEEDBACK =head2 Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bio-tools-phylo-paml/issues =head1 AUTHORS Jason Stajich Aaron Mackey Albert Vilella =head1 COPYRIGHT This software is copyright (c) by Jason Stajich , and by Aaron Mackey . This software is available under the same terms as the perl 5 programming language system itself. =cut Bio-Tools-Phylo-PAML-1.7.3/lib/Bio/Tools/Phylo/PAML.pm0000644000175000017500000020124613316145226022722 0ustar carandraugcarandraugpackage Bio::Tools::Phylo::PAML; $Bio::Tools::Phylo::PAML::VERSION = '1.7.3'; use utf8; use strict; use warnings; use vars qw($RSTFILENAME); use base qw(Bio::Root::Root Bio::Root::IO Bio::AnalysisParserI); use IO::String; use File::Spec; use Bio::TreeIO; use Bio::Tools::Phylo::PAML::Result; use Bio::LocatableSeq; use Bio::PrimarySeq; use Bio::Matrix::PhylipDist; use Bio::Tools::Phylo::PAML::ModelResult; # ABSTRACT: Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00 # AUTHOR: Jason Stajich # AUTHOR: Aaron Mackey # OWNER: Jason Stajich # OWNER: Aaron Mackey # LICENSE: Perl_5 # AUTHOR: Albert Vilella # AUTHOR: Sendu Bala # AUTHOR: Dave Messina BEGIN { $RSTFILENAME = 'rst'; # where to get the RST data from } sub new { my ( $class, @args ) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); my ($dir) = $self->_rearrange( [qw(DIR)], @args ); $self->{_dir} = $dir if defined $dir; return $self; } sub next_result { my ($self) = @_; my %data; # parse the RST file, if it doesn't exist or if dir is not set # this will just skip the parsing $self->_parse_rst(); my $idlookup; # a hashreference to SEQID (number) ==> 'SEQUENCENAME' # get the various codon and other sequence summary data, if necessary: $self->_parse_summary unless ( $self->{'_summary'} && !$self->{'_summary'}->{'multidata'} ); ## parse_summary reads the NG distance matrices which in the case ## of codeml and yn00 appear at the end of the file. This means ## that for those programs, there's nothing left to read, so all ## the code below is skipped, and we will return undef. Maybe in ## older versions of PAML (current version 4.9h) the order of ## output was different. Or maybe someone made parse_summary read ## more stuff and didn't notice that next_result was here. ## Anyway, rewinding to the start of the file after summary seems ## to fix all the issues. seek $self->_fh, 0, 0; # OK, depending on seqtype and runmode now, one of a few things can happen: my $seqtype = $self->{'_summary'}->{'seqtype'}; if ( $seqtype eq 'CODONML' || $seqtype eq 'AAML' ) { my $has_model_line = 0; while ( defined( $_ = $self->_readline ) ) { if ( $seqtype eq 'CODONML' && m/^pairwise comparison, codon frequencies:/ ) { # runmode = -2, CODONML $self->debug("pairwise Ka/Ks\n"); $self->_pushback($_); %data = $self->_parse_PairwiseCodon; last; } elsif ( $seqtype eq 'AAML' && m/^ML distances of aa seqs\.$/ ) { $self->_pushback($_); # get AA distances %data = ( '-AAMLdistmat' => $self->_parse_aa_dists() ); # $self->_pushback($_); # %data = $self->_parse_PairwiseAA; # last; } elsif ( m/^Model\s+(\d+)/ || ( ( !$has_model_line && m/^TREE/ ) && $seqtype eq 'CODONML' && ($self->{'_summary'}->{'version'} !~ /4/)) # last bit to keep PAML >= 4 from being caught here # bug 2482. Not sure this is the right fix, but tests # pass and the bug's test case passes. ) { $self->_pushback($_); my $model = $self->_parse_NSsitesBatch; push @{ $data{'-NSsitesresults'} }, $model; $has_model_line = 1; } elsif (m/for each branch/) { my %branch_dnds = $self->_parse_branch_dnds; if ( !defined $data{'-trees'} ) { $self->warn( "No trees have been loaded, can't do anything\n"); next; } my ($tree) = @{ $data{'-trees'} }; if ( !$tree || !ref($tree) || !$tree->isa('Bio::Tree::Tree') ) { $self->warn("no tree object already stored!\n"); next; } # These need to be added to the Node/branches while ( my ( $k, $v ) = each %branch_dnds ) { # we can probably do better by caching at some point my @nodes; for my $id ( split( /\.\./, $k ) ) { my @nodes_L = map { $tree->find_node( -id => $_ ) } @{ $idlookup->{$id} }; my $n = @nodes_L < 2 ? shift(@nodes_L) : $tree->get_lca(@nodes_L); if ( !$n ) { $self->warn("no node for $n\n"); } unless ( $n->is_Leaf && $n->id ) { $n->id($id); } push @nodes, $n; } my ( $parent, $child ) = @nodes; while ( my ( $kk, $vv ) = each %$v ) { $child->add_tag_value( $kk, $vv ); } } } elsif (m/^TREE/) { # runmode = 0 $self->_pushback($_); ( $data{'-trees'}, $idlookup ) = $self->_parse_Forestry; #last; } elsif (m/Heuristic tree search by stepwise addition$/) { # runmode = 3 $self->throw( -class => 'Bio::Root::NotImplemented', -text => "StepwiseAddition not yet implemented!" ); # $self->_pushback($_); # %data = $self->_parse_StepwiseAddition; # last; } elsif (m/Heuristic tree search by NNI perturbation$/) { # runmode = 4 $self->throw( -class => 'Bio::Root::NotImplemented', -text => "NNI Perturbation not yet implemented!" ); # $self->_pushback($_); # %data = $self->_parse_Perturbation; # last; } elsif (m/^stage 0:/) { # runmode = (1 or 2) $self->throw( -class => 'Bio::Root::NotImplemented', -text => "StarDecomposition not yet implemented!" ); $self->_pushback($_); %data = $self->_parse_StarDecomposition; last; } } } elsif ( $seqtype eq 'BASEML' ) { while ( defined( $_ = $self->_readline ) ) { if (/^Distances:/) { $self->_pushback($_); my ( $kappa, $alpha ) = $self->_parse_nt_dists(); %data = ( '-kappa_distmat' => $kappa, '-alpha_distmat' => $alpha ); } elsif (/^TREE/) { $self->_pushback($_); ( $data{'-trees'}, $idlookup ) = $self->_parse_Forestry; } } } elsif ( $seqtype eq 'YN00' ) { while ( $_ = $self->_readline ) { if ( m/^Estimation by the method|\(B\) Yang & Nielsen \(2000\) method/ ) { $self->_pushback($_); %data = $self->_parse_YN_Pairwise; last; } } } if (%data) { $data{'-version'} = $self->{'_summary'}->{'version'}; $data{'-seqs'} = $self->{'_summary'}->{'seqs'}; $data{'-patterns'} = $self->{'_summary'}->{'patterns'}; $data{'-ngmatrix'} = $self->{'_summary'}->{'ngmatrix'}; $data{'-codonpos'} = $self->{'_summary'}->{'codonposition'}; $data{'-codonfreq'} = $self->{'_summary'}->{'codonfreqs'}; $data{'-model'} = $self->{'_summary'}->{'model'}; $data{'-seqfile'} = $self->{'_summary'}->{'seqfile'}; $data{'-aadistmat'} = $self->{'_summary'}->{'aadistmat'}; $data{'-stats'} = $self->{'_summary'}->{'stats'}; $data{'-aafreq'} = $self->{'_summary'}->{'aafreqs'}; $data{'-ntfreq'} = $self->{'_summary'}->{'ntfreqs'}; $data{'-input_params'} = $self->{'_summary'}->{'inputparams'}; $data{'-rst'} = $self->{'_rst'}->{'rctrted_seqs'}; $data{'-rst_persite'} = $self->{'_rst'}->{'persite'}; $data{'-rst_trees'} = $self->{'_rst'}->{'trees'}; return Bio::Tools::Phylo::PAML::Result->new(%data); } else { return; } } sub _parse_summary { my ($self) = @_; # Depending on whether verbose > 0 or not, and whether the result # set comes from a multi-data run, the first few lines could be # various things; we're going to throw away any sequence data # here, since we'll get it later anyways # multidata ? : \n\nData set 1\n # verbose ? : cleandata ? : \nBefore deleting alignment gaps. \d sites\n # [ sequence printout ] # \nAfter deleting gaps. \d sites\n" # : [ sequence printout ] # CODONML (in paml 3.12 February 2002) <<-- what we want to see! my $SEQTYPES = qr( (?: (?: CODON | AA | BASE | CODON2AA ) ML ) | YN00 )x; my $line; $self->{'_already_parsed_seqs'} = $self->{'_already_parsed_seqs'} ? 1 : 0; my @lines; while ( $_ = $self->_readline ) { push @lines, $_; if (m/^($SEQTYPES) \s+ # seqtype: CODONML, AAML, BASEML, CODON2AAML, YN00, etc (?: \(in \s+ ([^\)]+?) \s* \) \s* )? # version: "paml 3.12 February 2002"; not present < 3.1 or YN00 (\S+) \s* # tree filename (?: (.+?) )? # model description (not there in YN00) \s* $ # trim any trailing space /ox ) { @{ $self->{'_summary'} }{qw(seqtype version seqfile model)} = ( $1, $2, $3, $4 ); # in 4.3, the model is on its own line if ( !defined $self->{'_summary'}->{'model'} ) { my $model_line = $self->_readline; chomp $model_line; if ($model_line =~ /^Model:/) { $self->{'_summary'}->{'model'} = $model_line; } } defined $self->{'_summary'}->{'model'} && $self->{'_summary'}->{'model'} =~ s/Model:\s+//; $self->_pushback($_) if $self->{'_summary'}->{'seqtype'} eq 'AAMODEL'; last; } elsif ((m/\s+?\d+?\s+?\d+?/) && ( $self->{'_already_parsed_seqs'} != 1 )) { $self->_parse_seqs; } elsif (m/^Data set \d$/) { $self->{'_summary'} = {}; $self->{'_summary'}->{'multidata'}++; } elsif (m/^Before\s+deleting\s+alignment\s+gaps/) { #Gap my ($phylip_header) = $self->_readline; $self->_parse_seqs; } elsif ( ( @lines >= 3 ) && ( $self->{'_already_parsed_seqs'} != 1 ) ) { #No gap # don't start parsing seqs yet if we're on a blank line # (gives another opportunity to match one of the other regexes) unless (/^\n$/) { $self->_parse_seqs; } } elsif ( (/Printing out site pattern counts/) && ( $self->{'_already_parsed_seqs'} != 1 ) ) { $self->_parse_patterns; } } unless ( defined $self->{'_summary'}->{'seqtype'} ) { $self->throw( -class => 'Bio::Root::NotImplemented', -text => 'Unknown format of PAML output did not see seqtype' ); } my $seqtype = $self->{'_summary'}->{'seqtype'}; if ( $seqtype eq "CODONML" ) { $self->_parse_inputparams(); # settings from the .ctl file # that get printed $self->_parse_patterns(); # codon patterns - not very interesting $self->_parse_seqs(); # the sequences data used for analysis $self->_parse_codoncts(); # counts and distributions of codon/nt # usage $self->_parse_codon_freqs(); # codon frequencies $self->_parse_distmat(); # NG distance matrices } elsif ( $seqtype eq "AAML" ) { $self->_parse_inputparams; $self->_parse_patterns(); $self->_parse_seqs(); # the sequences data used for analysis $self->_parse_aa_freqs(); # AA frequencies # get AA distances $self->{'_summary'}->{'aadistmat'} = $self->_parse_aa_dists(); } elsif ( $seqtype eq "CODON2AAML" ) { $self->throw( -class => 'Bio::Root::NotImplemented', -text => 'CODON2AAML parsing not yet implemented!' ); } elsif ( $seqtype eq "BASEML" ) { $self->_parse_patterns(); $self->_parse_seqs(); $self->_parse_nt_freqs(); } elsif ( $seqtype eq "YN00" ) { $self->_parse_codon_freqs(); $self->_parse_codoncts(); $self->_parse_distmat(); # NG distance matrices } else { $self->throw( -class => 'Bio::Root::NotImplemented', -text => 'Unknown seqtype, not yet implemented!', -value => $seqtype ); } } sub _parse_inputparams { my ($self) = @_; while ( defined( $_ = $self->_readline ) ) { if (/^((?:Codon frequencies)|(?:Site-class models))\s*:\s+(.+)/) { my ( $param, $val ) = ( $1, $2 ); $self->{'_summary'}->{'inputparams'}->{$param} = $val; } elsif (/^\s+$/) { next; } elsif ( /^ns\s+=\s+/ || /^Frequencies/ ) { $self->_pushback($_); last; } } } sub _parse_codon_freqs { my ($self) = @_; my ( $okay, $done ) = ( 0, 0 ); while ( defined( $_ = $self->_readline ) ) { if (/^Nei|\(A\) Nei/) { $self->_pushback($_); last } last if ($done); next if (/^\s+/); next unless ( $okay || /^Codon position x base \(3x4\) table\, overall/ ); $okay = 1; if (s/^position\s+(\d+):\s+//) { my $pos = $1; s/\s+$//; my @bases = split; foreach my $str (@bases) { my ( $base, $freq ) = split( /:/, $str, 2 ); $self->{'_summary'}->{'codonposition'}->[ $pos - 1 ]->{$base} = $freq; } $done = 1 if $pos == 3; } } $done = 0; while ( defined( $_ = $self->_readline ) ) { if (/^Nei\s\&\sGojobori|\(A\)\sNei-Gojobori/) { $self->_pushback($_); last; } last if ($done); if (/^Codon frequencies under model, for use in evolver/) { while ( defined( $_ = $self->_readline ) ) { last if (/^\s+$/); s/^\s+//; s/\s+$//; push @{ $self->{'_summary'}->{'codonfreqs'} }, [split]; } $done = 1; } } } sub _parse_aa_freqs { my ($self) = @_; my ( $okay, $done, $header ) = ( 0, 0, 0 ); my (@bases); my $numseqs = scalar @{ $self->{'_summary'}->{'seqs'} || [] }; while ( defined( $_ = $self->_readline ) ) { if ( /^TREE/ || /^AA distances/ ) { $self->_pushback($_); last; } last if ($done); next if ( /^\s+$/ || /^\(Ambiguity/ ); if (/^Frequencies\./) { $okay = 1; } elsif ( !$okay ) { # skip till we see 'Frequencies. next; } elsif ( !$header ) { s/^\s+//; # remove leading whitespace @bases = split; # get an array of the all the aa names $header = 1; $self->{'_summary'}->{'aafreqs'} = {}; # reset/clear values next; } elsif ( /^\#\s+constant\s+sites\:\s+ (\d+)\s+ # constant sites \(\s*([\d\.]+)\s*\%\s*\)/x ) { $self->{'_summary'}->{'stats'}->{'constant_sites'} = $1; $self->{'_summary'}->{'stats'}->{'constant_sites_percentage'} = $2; } elsif (/^ln\s+Lmax\s+\(unconstrained\)\s+\=\s+(\S+)/x) { $self->{'_summary'}->{'stats'}->{'loglikelihood'} = $1; $done = 1; # done for sure } else { my ( $seqname, @freqs ) = split; my $basect = 0; foreach my $f (@freqs) { # this will also store 'Average' $self->{'_summary'}->{'aafreqs'}->{$seqname} ->{ $bases[ $basect++ ] } = $f; } } } } # This is for parsing the automatic tree output sub _parse_StarDecomposition { my ($self) = @_; my %data; return %data; } sub _parse_aa_dists { my ($self) = @_; my ( $okay, $seen, $done ) = ( 0, 0, 0 ); my ( %matrix, @names, @values ); my $numseqs = scalar @{ $self->{'_summary'}->{'seqs'} || [] }; my $type = ''; while ( defined( $_ = $self->_readline ) ) { last if $done; if (/^TREE/) { $self->_pushback($_); last; } if (/^\s+$/) { last if ($seen); next; } if (/^(AA|ML) distances/) { $okay = 1; $type = $1; next; } s/\s+$//g; # remove trailing space if ($okay) { my ( $seqname, @vl ) = split; $seen = 1; my $i = 0; # hacky workaround to problem with 3.14 aaml if ( $type eq 'ML' && !@names && # first entry @vl ) { # not empty push @names, $self->{'_summary'}->{'seqs'}->[0]->display_id; } for my $s (@names) { last unless @vl; $matrix{$seqname}->{$s} = $matrix{$s}->{$seqname} = shift @vl; } push @names, $seqname; $matrix{$seqname}->{$seqname} = 0; } $done = 1 if ( scalar @names == $numseqs ); } my %dist; my $i = 0; @values = (); foreach my $lname (@names) { my @row; my $j = 0; foreach my $rname (@names) { my $v = $matrix{$lname}->{$rname}; $v = $matrix{$rname}->{$lname} unless defined $v; push @row, $v; $dist{$lname}{$rname} = [ $i, $j++ ]; } $i++; push @values, \@row; } return new Bio::Matrix::PhylipDist( -program => $self->{'_summary'}->{'seqtype'}, -matrix => \%dist, -names => \@names, -values => \@values ); } sub _parse_patterns { my ($self) = @_; my ( $patternct, @patterns, $ns, $ls ); return if exists $self->{'_summary'}->{'patterns'}; while ( defined( $_ = $self->_readline ) ) { if ( /^Codon\s+(usage|position)/ || /Model/ ) { $self->_pushback($_); last; } elsif ($patternct) { # last unless ( @patterns == $patternct ); last if (/^\s+$/); s/^\s+//; push @patterns, split; } elsif (/^ns\s+\=\s*(\d+)\s+ls\s+\=\s*(\d+)/) { ( $ns, $ls ) = ( $1, $2 ); } elsif (/^\# site patterns \=\s*(\d+)/) { $patternct = $1; } else { # $self->debug("Unknown line: $_"); } } $self->{'_summary'}->{'patterns'} = { -patterns => \@patterns, -ns => $ns, -ls => $ls }; } sub _parse_seqs { # this should in fact be packed into a Bio::SimpleAlign object instead of # an array but we'll stay with this for now my ($self) = @_; # Use this flag to deal with paml 4 vs 3 differences # In PAML 4 the sequences precede the CODONML|BASEML|AAML # while in PAML3 the files start off with this return 1 if $self->{'_already_parsed_seqs'}; my ( @firstseq, @seqs ); while ( defined( $_ = $self->_readline ) ) { if (/^(Printing|After|TREE|Codon)/) { $self->_pushback($_); last; } last if ( /^\s+$/ && @seqs > 0 ); next if (/^\s+$/); next if (/^\d+\s+$/); # we are reading PHYLIP format my ( $name, $seqstr ) = split( /\s+/, $_, 2 ); $seqstr =~ s/\s+//g; # remove whitespace unless (@firstseq) { @firstseq = split( //, $seqstr ); push @seqs, Bio::LocatableSeq->new( -display_id => $name, -seq => $seqstr ); } else { my $i = 0; my $v; while ( ( $v = index( $seqstr, '.', $i ) ) >= $i ) { # replace the '.' with the correct seq from the substr( $seqstr, $v, 1, $firstseq[$v] ); $i = $v; } push @seqs, Bio::LocatableSeq->new( -display_id => $name, -seq => $seqstr ); } } if ( @seqs > 0 ) { $self->{'_summary'}->{'seqs'} = \@seqs; $self->{'_already_parsed_seqs'} = 1; } 1; } sub _parse_codoncts { } sub _parse_distmat { my ($self) = @_; my @results; my $ver = 3.14; my $firstseq, my $secondseq; while ( defined( $_ = $self->_readline ) ) { next if /^\s+$/; # We need to get the names of the sequences if this is from YN00: if (/^\(A\)\sNei-Gojobori\s\(1986\)\smethod/) { $ver = 3.15; while ( defined( $_ = $self->_readline ) ) { if ($_ =~ m/.*\d+?\.\d+?\s*\(.*/) { $secondseq = $_; last; } $firstseq = $_; } } last; } #return unless (/^Nei\s*\&\s*Gojobori/); # skip the next 3 lines if ( $self->{'_summary'}->{'seqtype'} eq 'CODONML' ) { $self->_readline; $self->_readline; $self->_readline; } my $seqct = 0; my @seqs; if ( $self->{'_summary'}->{'seqtype'} eq 'YN00' ) { if ($firstseq) { $firstseq =~ s/(.+?)\s+.*/$1/; $secondseq =~ s/(.+?)\s+.*/$1/; chomp $firstseq; chomp $secondseq; push @seqs, Bio::PrimarySeq->new( -display_id => $firstseq ); push @seqs, Bio::PrimarySeq->new( -display_id => $secondseq ); } } while ( defined( $_ = $self->_readline ) ) { last if ( /^\s+$/ && exists $self->{'_summary'}->{'ngmatrix'} ); next if ( /^\s+$/ || /^NOTE:/i ); chomp; my ( $seq, $rest ); if ( $self->{'_summary'}->{'seqtype'} eq 'YN00' ) { ( $seq, $rest ) = split( /\s+/, $_, 2 ); } else { $_ =~ m/(.+?)\s*(-*\d+?\.\d+?.*)/; $seq = $1; $rest = $2; } $rest = '' unless defined $rest; # get rid of empty messages my $j = 0; if ( $self->{'_summary'}->{'seqtype'} eq 'YN00' ) { push @seqs, Bio::PrimarySeq->new( -display_id => $seq ); } while ($rest && $rest =~ /(\-?\d+(\.\d+)?)\s*\(\-?(\d+(\.\d+)?)\s+(\-?\d+(\.\d+)?)\)/g ) { $self->{'_summary'}->{'ngmatrix'}->[ $j++ ]->[$seqct] = { 'omega' => $1, 'dN' => $3, 'dS' => $5 }; } $seqct++; } if ( $self->{'_summary'}->{'seqtype'} eq 'YN00' && @seqs ) { $self->{'_summary'}->{'seqs'} = \@seqs; } 1; } sub _parse_PairwiseCodon { my ($self) = @_; my @result; my ( $a, $b, $log, $model, $t, $kappa, $omega, $fixedkappa ); # check to see if we have a fixed kappa: if ( $self->{'_summary'}->{'model'} =~ /kappa = (\d+?\.\d+?) fixed/) { $fixedkappa = $1; } while ( defined( $_ = $self->_readline ) ) { if (/^pairwise comparison, codon frequencies\:\s*(\S+)\./) { $model = $1; } # 1st line of a pair block, e.g. # 2 (all_c7259) ... 1 (all_s57600) elsif (/^(\d+)\s+\((\S+)\)\s+\.\.\.\s+(\d+)\s+\((\S+)\)/) { ( $a, $b ) = ( $1, $3 ); } # 2nd line of a pair block, e.g. # lnL = -126.880601 elsif (/^lnL\s+\=\s*(\-?\d+(\.\d+)?)/) { $log = $1; if ( defined( $_ = $self->_readline ) ) { # 3rd line of a pair block, e.g. # 0.19045 2.92330 0.10941 s/^\s+//; ( $t, $kappa, $omega ) = split; # if there was a fixed kappa, there will only be two values here ($t, $omega) and $kappa = $fixedkappa. if ($omega eq "") { $omega = $kappa; $kappa = $fixedkappa; } } } # 5th line of a pair block, e.g. # t= 0.1904 S= 5.8 N= 135.2 dN/dS= 0.1094 dN= 0.0476 dS= 0.4353 # OR lines like (note last field; this includes a fix for bug #3040) # t= 0.0439 S= 0.0 N= 141.0 dN/dS= 0.1626 dN= 0.0146 dS= nan elsif (m/^t\=\s*(\d+(\.\d+)?)\s+/) { # Breaking out each piece individually so that you can see # what each regexp actually looks for my $parse_string = $_; $parse_string =~ m/.*t\s*\=\s*(\d+?\.\d+?)\s/; my $temp_t = $1; $parse_string =~ m/\sS\s*\=\s*(\d+?\.\d+?)\s/; my $temp_S = $1; $parse_string =~ m/\sN\s*\=\s*(\d+?\.\d+?)\s/; my $temp_N = $1; $parse_string =~ m/\sdN\/dS\s*\=\s*(\d+?\.\d+?)\s/; my $temp_omega = $1; $parse_string =~ m/\sdN\s*\=\s*(\d+?\.\d+?)\s/; my $temp_dN = $1; $parse_string =~ m/\sdS\s*\=\s*(.+)\s/; my $temp_dS = $1; $result[ $b - 1 ]->[ $a - 1 ] = { 'lnL' => $log, 't' => defined $t && length($t) ? $t : $temp_t, 'S' => $temp_S, 'N' => $temp_N, 'kappa' => $kappa, 'omega' => defined $omega && length($omega) ? $omega : $temp_omega, 'dN' => $temp_dN, 'dS' => $temp_dS }; } # 4th line of a pair block (which is blank) elsif (/^\s+$/) { next; } elsif (/^\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)/) { } else { $self->debug("unknown line: $_"); } } return ( -mlmatrix => \@result ); } sub _parse_YN_Pairwise { my ($self) = @_; my @result; while ( defined( $_ = $self->_readline ) ) { last if (/^seq\.\s+seq\./); } while ( defined( $_ = $self->_readline ) ) { if ( m/^\s+(\d+)\s+ # seq # (\d+)\s+ # seq # (\d+(\.\d+))\s+ # S (\d+(\.\d+))\s+ # N (\d+(\.\d+))\s+ # t (\d+(\.\d+))\s+ # kappa (\d+(\.\d+))\s+ # omega \-??(\d+(\.\d+))\s+ # dN \+\-\s+ \-??(\d+(\.\d+))\s+ # dN SE \-??(\d+(\.\d+))\s+ # dS \+\-\s+ \-??(\d+(\.\d+))\s+ # dS SE /ox ) { $result[ $2 - 1 ]->[ $1 - 1 ] = { 'S' => $3, 'N' => $5, 't' => $7, 'kappa' => $9, 'omega' => $11, 'dN' => $13, 'dN_SE' => $15, 'dS' => $17, 'dS_SE' => $19, }; } elsif (/^\s+$/) { next; } elsif (/^\(C\) LWL85, LPB93 & LWLm methods/) { $self->_pushback($_); last; } } return ( -mlmatrix => \@result ); } sub _parse_Forestry { my ($self) = @_; my ( $instancecount, $num_param, $loglikelihood, $score, $done, $treelength ) = ( 0, 0, 0, 0, 0, 0 ); my $okay = 0; my ( @ids, %match, @branches, @trees ); while ( defined( $_ = $self->_readline ) ) { last if $done; if (s/^TREE\s+\#\s*\d+:\s+//) { ($score) = (s/MP\s+score\:\s+(\S+)\s+$//); @ids = /(\d+)[\,\)]/g; } elsif (/^Node\s+\&/ || /^\s+N37/ || /^(CODONML|AAML|YN00|BASEML)/ || /^\*\*/ || /^Detailed output identifying parameters/ ) { $self->_pushback($_); $done = 1; last; } elsif (/^tree\s+length\s+\=\s+(\S+)/) { $treelength = $1; # not going to store this for now # as it is directly calculated from # $tree->total_branch_length; } elsif (/^\s*lnL\(.+np\:\s*(\d+)\)\:\s+(\S+)/) { # elsif( /^\s*lnL\(.+\)\:\s+(\S+)/ ) { ( $num_param, $loglikelihood ) = ( $1, $2 ); } elsif (/^\(/) { s/([\,:])\s+/$1/g; my $treestr = IO::String->new($_); my $treeio = Bio::TreeIO->new( -fh => $treestr, -format => 'newick' ); my $tree = $treeio->next_tree; if ($tree) { $tree->score($loglikelihood); $tree->id("num_param:$num_param"); if ( $okay > 0 ) { # we don't save the trees with the number labels if ( !%match && @ids ) { my $i = 0; for my $m (/([^():,]+):/g) { $match{ shift @ids } = [$m]; } my %grp; while ( my $br = shift @branches ) { my ( $parent, $child ) = @$br; if ( $match{$child} ) { push @{ $match{$parent} }, @{ $match{$child} }; } else { push @branches, $br; } } if ( $self->verbose > 1 ) { for my $k ( sort { $a <=> $b } keys %match ) { $self->debug( "$k -> ", join( ",", @{ $match{$k} } ), "\n" ); } } } # Associate SEs to nodes using tags if ( defined( $self->{_SEs} ) ) { my @SEs = split( " ", $self->{_SEs} ); my $i = 0; foreach my $parent_id ( map { /\d+\.\.(\d+)/ } split( " ", $self->{_branch_ids} ) ) { my @nodes; my @node_ids = @{ $match{$parent_id} }; my @nodes_L = map { $tree->find_node( -id => $_ ) } @node_ids; my $n = @nodes_L < 2 ? shift(@nodes_L) : $tree->get_lca(@nodes_L); if ( !$n ) { $self->warn( "no node could be found for node in SE assignation (no lca?)" ); } $n->add_tag_value( 'SE', $SEs[$i] ); $i++; } } push @trees, $tree; } } $okay++; } elsif (/^SEs for parameters/) { my $se_line = $self->_readline; $se_line =~ s/\n//; $self->{_SEs} = $se_line; } elsif (/^\s*\d+\.\.\d+/) { push @branches, map { [ split( /\.\./, $_ ) ] } split; my $ids = $_; $ids =~ s/\n//; $self->{_branch_ids} = $ids; } } return \@trees, \%match; } sub _parse_NSsitesBatch { my $self = shift; my ( %data, $idlookup ); my ( $okay, $done ) = ( 0, 0 ); while ( defined( $_ = $self->_readline ) ) { last if $done; next if /^\s+$/; next unless ( $okay || /^Model\s+\d+/ || /^TREE/ ); if (/^Model\s+(\d+)/) { if ($okay) { # this only happens if $okay was already 1 and # we hit a Model line $self->_pushback($_); $done = 1; } else { chomp; $data{'-model_num'} = $1; ( $data{'-model_description'} ) = (/\:\s+(.+)/); $okay = 1; } } elsif (/^Time used\:\s+(\S+)/) { $data{'-time_used'} = $1; $done = 1; } elsif (/^kappa\s+\(ts\/tv\)\s+\=\s+(\S+)/) { $data{'-kappa'} = $1; } elsif (/^TREE/) { $self->_pushback($_); ( $data{'-trees'}, $idlookup ) = $self->_parse_Forestry; if ( defined $data{'-trees'} && scalar @{ $data{'-trees'} } ) { $data{'-likelihood'} = $data{'-trees'}->[0]->score; } $okay = 1; } elsif (/^omega\s+\(dn\/ds\)\s+\=\s+(\S+)/i) { # for M0 (single ratio for the entire tree) # explicitly put '1.00000' rather than '1', because \d+\.\d{5} # is reported in all other cases. my @p = (q/1.00000/); # since there is only one class, my @w = $1; $data{'-dnds_site_classes'} = { 'p' => \@p, 'w' => \@w }; # since no K=X is provided, put 1 here $data{q/-num_site_classes/} = 1; } elsif ( /^(Naive Empirical Bayes)|(Bayes Empirical Bayes)|(Positively\sselected\ssites)/i ) { $self->_pushback($_); my ( $sites, $neb, $beb ) = $self->_parse_Pos_selected_sites; $data{'-pos_sites'} = $sites; $data{'-neb_sites'} = $neb; $data{'-beb_sites'} = $beb; } elsif (/^dN/i) { if (/K\=(\d+)/) { $data{'-num_site_classes'} = $1; while ( $_ = $self->_readline ) { unless ( $_ =~ /^\s+$/ ) { $self->_pushback($_); last; } } if (/^site class/) { $self->_readline; my $tmp = $self->_readline; my @p = $tmp =~ /(\d+\.\d{5})/g; $tmp = $self->_readline; my @b_w = $tmp =~ /(\d+\.\d{5})/g; $tmp = $self->_readline; my @f_w = $tmp =~ /(\d+\.\d{5})/g; my @w; foreach my $i ( 0 .. $#b_w ) { push @w, { q/background/ => $b_w[$i], q/foreground/ => $f_w[$i] }; } $data{'-dnds_site_classes'} = { q/p/ => \@p, q/w/ => \@w }; } else { my $tmp = $self->_readline; my @p = $tmp =~ /(\d+\.\d{5})/g; $tmp = $self->_readline; my @w = $tmp =~ /(\d+\.\d{5})/g; $data{'-dnds_site_classes'} = { 'p' => \@p, 'w' => \@w }; } } elsif (/for each branch/) { my %branch_dnds = $self->_parse_branch_dnds; if ( !defined $data{'-trees'} ) { $self->warn( "No trees have been loaded, can't do anything\n"); next; } my ($tree) = @{ $data{'-trees'} }; if ( !$tree || !ref($tree) || !$tree->isa('Bio::Tree::Tree') ) { $self->warn("no tree object already stored!\n"); next; } # These need to be added to the Node/branches while ( my ( $k, $v ) = each %branch_dnds ) { # we can probably do better by caching at some point my @nodes; for my $id ( split( /\.\./, $k ) ) { my @nodes_L = map { $tree->find_node( -id => $_ ) } @{ $idlookup->{$id} }; my $n = @nodes_L < 2 ? shift(@nodes_L) : $tree->get_lca(@nodes_L); if ( !$n ) { $self->warn( "no node could be found for $id (no lca?)"); } unless ( $n->is_Leaf && $n->id ) { $n->id($id); } push @nodes, $n; } my ( $parent, $child ) = @nodes; while ( my ( $kk, $vv ) = each %$v ) { $child->add_tag_value( $kk, $vv ); } } } } elsif (/^Parameters in beta:/) { $_ = $self->_readline; # need the next line if (/p\=\s+(\S+)\s+q\=\s+(\S+)/) { $data{'-shape_params'} = { 'shape' => 'beta', 'p' => $1, 'q' => $2 }; } else { $self->warn("unparseable beta parameters: $_"); } } elsif (/^Parameters in beta\&w\>1:/) { # Parameters in beta&w>1: # p0= 1.00000 p= 0.07642 q= 0.85550 # (p1= 0.00000) w= 1.00000 $_ = $self->_readline; # need the next line my ( $p0, $p, $q, $p1, $w ); if (/p0\=\s+(\S+)\s+p\=\s+(\S+)\s+q\=\s+(\S+)/) { $p0 = $1; $p = $2; $q = $3; } else { $self->warn("unparseable beta parameters: $_"); } $_ = $self->_readline; # need the next line if (/\(p1\=\s+(\S+)\)\s+w\=\s*(\S+)/) { $p1 = $1; $w = $2; $data{'-shape_params'} = { 'shape' => 'beta', 'p0' => $p0, 'p' => $p, 'q' => $q, 'p1' => $p1, 'w' => $w }; } else { $self->warn("unparseable beta parameters: $_"); } } elsif (/^alpha\s+\(gamma\)\s+\=\s+(\S+)/) { my $gamma = $1; $_ = $self->_readline; my ( @r, @f ); if (s/^r\s+\(\s*\d+\)\:\s+//) { @r = split; } $_ = $self->_readline; if (s/^f\s*\:\s+//) { @f = split; } $data{'-shape_params'} = { 'shape' => 'alpha', 'gamma' => $gamma, 'r' => \@r, 'f' => \@f }; } } return new Bio::Tools::Phylo::PAML::ModelResult(%data); } sub _parse_Pos_selected_sites { my $self = shift; my $okay = 0; my (%sites) = ( 'default' => [], 'neb' => [], 'beb' => [] ); my $type = 'default'; while ( defined( $_ = $self->_readline ) ) { next if ( /^\s+$/ || /^\s+Pr\(w\>1\)/ ); if ( /^Time used/ || /^TREE/ ) { $self->_pushback($_); last; } if (/^Naive Empirical Bayes/i) { $type = 'neb'; } elsif (/^Bayes Empirical Bayes/i) { $type = 'beb'; } elsif (/^Positively selected sites/) { $okay = 1; } elsif ( $okay && /^\s+(\d+)\s+(\S+)\s+(\-?\d+(?:\.\d+)?)(\**)\s+(\-?\d+(?:\.\d+)?)\s+\+\-\s+(\-?\d+(?:\.\d+)?)/ ) { my $signif = $4; $signif = '' unless defined $signif; push @{ $sites{$type} }, [ $1, $2, $3, $signif, $5, $6 ]; } elsif ( $okay && /^\s+(\d+)\s+(\S+)\s+(\-?\d*(?:.\d+))(\**)\s+(\-?\d+(?:\.\d+)?)/ ) { my $signif = $4; $signif = '' unless defined $signif; push @{ $sites{$type} }, [ $1, $2, $3, $signif, $5 ]; } elsif ( $okay && /^\s+(\d+)\s+(\S)\s+([\d\.\-\+]+)(\**)/ ) { my $signif = $4; $signif = '' unless defined $signif; push @{ $sites{$type} }, [ $1, $2, $3, $signif ]; } } return ( $sites{'default'}, $sites{'neb'}, $sites{'beb'} ); } sub _parse_branch_dnds { my $self = shift; my ($okay) = (0); my %branch_dnds; my @header; while ( defined( $_ = $self->_readline ) ) { next if (/^\s+$/); next unless ( $okay || /^\s+branch\s+t/ ); if (/^\s+branch\s+(.+)/) { s/^\s+//; @header = split( /\s+/, $_ ); $okay = 1; } elsif (/^\s*(\d+\.\.\d+)/) { my $branch = $1; s/^\s+//; my $i = 0; # fancyness just maps the header names like 't' or 'dN' # into the hash so we get at the end of the day # 't' => 0.067 # 'dN'=> 0.001 $branch_dnds{$branch} = { map { $header[ $i++ ] => $_ } split }; } else { $self->_pushback($_); last; } } return %branch_dnds; } #baseml stuff sub _parse_nt_freqs { my ($self) = @_; my ( $okay, $done, $header ) = ( 0, 0, 0 ); my (@bases); my $numseqs = scalar @{ $self->{'_summary'}->{'seqs'} || [] }; while ( defined( $_ = $self->_readline ) ) { if ( /^TREE/ || /^Distances/ ) { $self->_pushback($_); last } last if ($done); next if ( /^\s+$/ || /^\(Ambiguity/ ); if (/^Frequencies\./) { $okay = 1; } elsif ( !$okay ) { # skip till we see 'Frequencies. next; } elsif ( !$header ) { s/^\s+//; # remove leading whitespace @bases = split; # get an array of the all the aa names $header = 1; $self->{'_summary'}->{'ntfreqs'} = {}; # reset/clear values next; } elsif ( /^\#\s+constant\s+sites\:\s+ (\d+)\s+ # constant sites \(\s*([\d\.]+)\s*\%\s*\)/ox ) { $self->{'_summary'}->{'stats'}->{'constant_sites'} = $1; $self->{'_summary'}->{'stats'}->{'constant_sites_percentage'} = $2; } elsif (/^ln\s+Lmax\s+\(unconstrained\)\s+\=\s+(\S+)/ox) { $self->{'_summary'}->{'stats'}->{'loglikelihood'} = $1; $done = 1; # done for sure } else { my ( $seqname, @freqs ) = split; my $basect = 0; foreach my $f (@freqs) { # this will also store 'Average' $self->{'_summary'}->{'ntfreqs'}->{$seqname} ->{ $bases[ $basect++ ] } = $f; } } } } sub _parse_nt_dists { my ($self) = @_; my ( $okay, $seen, $done ) = ( 0, 0, 0 ); my ( %matrix, @names ); my $numseqs = scalar @{ $self->{'_summary'}->{'seqs'} || [] }; my $type = ''; while ( defined( $_ = $self->_readline ) ) { if (/^TREE/) { $self->_pushback($_); last; } last if $done; next if (/^This matrix is not used in later/); if (/^\s+$/) { last if ($seen); next; } if (/^Distances:(\S+)\s+\(([^\)]+)\)\s+\(alpha set at (\-?\d+\.\d+)\)/) { $okay = 1; $type = $1; next; } s/\s+$//g; # remove trailing space if ($okay) { my ( $seqname, $vl ) = split( /\s+/, $_, 2 ); $seen = 1; my $i = 0; if ( defined $vl ) { while ( $vl =~ /(\-?\d+\.\d+)\s*\(\s*(\-?\d+\.\d+)\s*\)\s*/g ) { my ( $kappa, $alpha ) = ( $1, $2 ); $matrix{$seqname}{ $names[$i] } = $matrix{ $names[$i] }{$seqname} = [ $kappa, $alpha ]; $i++; } unless ($i) { $self->warn("no matches for $vl\n"); } } push @names, $seqname; $matrix{$seqname}->{$seqname} = [ 0, 0 ]; } $done = 1 if ( scalar @names == $numseqs ); } my %dist; my $i = 0; my ( @kvalues, @avalues ); foreach my $lname (@names) { my ( @arow, @krow ); my $j = 0; foreach my $rname (@names) { my $v = $matrix{$lname}{$rname}; push @krow, $v->[0]; # kappa values push @arow, $v->[1]; # alpha $dist{$lname}{$rname} = [ $i, $j++ ]; } $i++; push @kvalues, \@krow; push @avalues, \@arow; } return ( Bio::Matrix::PhylipDist->new( -program => $self->{'_summary'}->{'seqtype'}, -matrix => \%dist, -names => \@names, -values => \@kvalues ), Bio::Matrix::PhylipDist->new( -program => $self->{'_summary'}->{'seqtype'}, -matrix => \%dist, -names => \@names, -values => \@avalues ) ); } # BASEML sub _parse_rate_parametes { my $self = shift; my (%rate_parameters); while ( defined( $_ = $self->_readline ) ) { if (/^Rate\s+parameters:\s+/) { s/\s+$//; $rate_parameters{'rate_parameters'} = [ split( /\s+/, $_ ) ]; } elsif (/^Base\s+frequencies:\s+/) { s/\s+$//; $rate_parameters{'base_frequencies'} = [ split( /\s+/, $_ ) ]; } elsif ( m/^Rate\s+matrix\s+Q,\s+Average\s+Ts\/Tv\s+(\([^\)+]+\))?\s*\=\s+ (\-?\d+\.\d+)/x ) { $rate_parameters{'average_TsTv'} = $1; while ( defined( $_ = $self->_readline ) ) { # short circuit last if (/^\s+$/); if (/^alpha/) { $self->_pushback($_); last; } s/^\s+//; s/\s+$//; push @{ $rate_parameters{'rate_matrix_Q'} }, [split]; } } elsif (/^alpha\s+\(gamma,\s+K=\s*(\d+)\s*\)\s*\=\s*(\-?\d+\.\d+)/) { $rate_parameters{'K'} = $1; $rate_parameters{'alpha'} = $2; } elsif (s/^(r|f):\s+//) { my ($p) = $1; s/\s+$//; $rate_parameters{$p} = [split]; } } } # RST parsing sub _parse_rst { my ($self) = @_; return unless $self->{'_dir'} && -d $self->{'_dir'} && -r $self->{'_dir'}; my $rstfile = File::Spec->catfile( $self->{'_dir'}, $RSTFILENAME ); return unless -e $rstfile && !-z $rstfile; my $rstio = Bio::Root::IO->new( -file => $rstfile ); # define whatever data structures you need to store the data # key points are to reuse existing bioperl objs (like Bio::Seq) # where appropriate my ( @firstseq, @seqs, @trees, @per_site_prob ); my $count; while ( defined( $_ = $rstio->_readline ) ) { # implement the parsing here if (/^TREE\s+\#\s+(\d+)/) { while ( defined( $_ = $rstio->_readline ) ) { if (/tree\s+with\s+node\s+labels\s+for/) { my $tree = Bio::TreeIO->new( -noclose => 1, -fh => $rstio->_fh, -format => 'newick' )->next_tree; # cleanup leading/trailing whitespace for my $n ( $tree->get_nodes ) { my $id = $n->id; $id =~ s/^\s+//; $id =~ s/\s+$//; $n->id($id); if ( defined( my $blen = $n->branch_length ) ) { $blen =~ s/^\s+//; $blen =~ s/\s+$//; $n->branch_length($blen); } } push @trees, $tree; last; } } } elsif (/^Prob\sof\sbest\scharacter\sat\seach\snode,\slisted\sby\ssite/) { $self->{'_rst'}->{'persite'} = []; while ( defined( $_ = $rstio->_readline ) ) { next if ( /^Site/i || /^\s+$/ ); if (s/^\s+(\d+)\s+(\d+)\s+([^:]+)\s*:\s*(.+)//) { my ( $sitenum, $freq, $extant, $ancestral ) = ( $1, $2, $3, $4 ); my ( @anc_site, @extant_site ); @extant_site = {}; while ( $extant =~ s/^([A-Z\-]{3})\s+\(([A-Z*])\)\s+//g ) { push @extant_site, { 'codon' => $1, 'aa' => $2 }; } while ( $ancestral =~ s/^([A-Z\-]{3})\s+([A-Z*])\s+ # codon AA (\S+)\s+ # Prob \(([A-Z*])\s+(\S+)\)\s*//xg # AA Prob ) { push @anc_site, { 'codon' => $1, 'aa' => $2, 'prob' => $3, 'Yang95_aa' => $4, 'Yang95_aa_prob' => $5 }; } # saving persite $self->{'_rst'}->{'persite'}->[$sitenum] = [ @extant_site, @anc_site ]; } elsif (/^Summary\sof\schanges\salong\sbranches\./) { last; } } } elsif (/^Check\sroot\sfor\sdirections\sof\schange\./ || /^Summary\sof\schanges\salong\sbranches\./ ) { my ( @branches, @branch2node, $branch, $node ); my $tree = $trees[-1]; if ( !$tree ) { $self->warn("No tree built before parsing Branch changes\n"); last; } my @nodes = ( map { $_->[0] } sort { $a->[1] <=> $b->[1] } map { [ $_, $_->id =~ /^(\d+)\_?/ ] } $tree->get_nodes ); unshift @nodes, undef; # fake first node so that index will match nodeid while ( defined( $_ = $rstio->_readline ) ) { next if /^\s+$/; if (m/^List\sof\sextant\sand\sreconstructed\ssequences/) { $rstio->_pushback($_); last; } elsif (/^Branch\s+(\d+):\s+(\d+)\.\.(\d+)\s+/) { my ( $left, $right ); ( $branch, $left, $right ) = ( $1, $2, $3 ); ($node) = $nodes[$right]; if ( !$node ) { $self->warn( "cannot find $right in $tree ($branch $left..$right)\n" ); last; } if (/\(n=\s*(\S+)\s+s=\s*(\S+)\)/) { $node->add_tag_value( 'n', $1 ); $node->add_tag_value( 's', $2 ); } $branch2node[$branch] = $right; } elsif ( /^\s+(\d+)\s+([A-Z*])\s+(\S+)\s+\-\>\s+([A-Z*])\s+(\S+)?/) { my ( $site, $anc, $aprob, $derived, $dprob ) = ( $1, $2, $3, $4, $5 ); if ( !$node ) { $self->warn("no branch line was previously parsed!"); next; } my %c = ( 'site' => $site, 'anc_aa' => $anc, 'anc_prob' => $aprob, 'derived_aa' => $derived, ); $c{'derived_prob'} = $dprob if defined $dprob; $node->add_tag_value( 'changes', \%c ); } } } elsif ( /^Overall\s+accuracy\s+of\s+the\s+(\d+)\s+ancestral\s+sequences:/) { my $line = $rstio->_readline; $line =~ s/^\s+//; $line =~ s/\s+$//; my @overall_site = split( /\s+/, $line ); # skip next 2 lines, want the third for ( 1 .. 3 ) { $line = $rstio->_readline; } $line =~ s/^\s+//; $line =~ s/\s+$//; my @overall_seq = split( /\s+/, $line ); if ( @overall_seq != @overall_site || @overall_seq != @seqs ) { $self->warn( "out of sync somehow seqs, site scores don't match\n"); $self->warn("@seqs @overall_seq @overall_site\n"); } for (@seqs) { $_->description( sprintf( "overall_accuracy_site=%s overall_accuracy_seq=%s", shift @overall_site, shift @overall_seq ) ); } } elsif (m/^List of extant and reconstructed sequences/o) { my $seqcount = 0; while ( defined( $_ = $rstio->_readline ) ) { last if (/^Overall accuracy of the/); if (/^\s+$/) { last if $seqcount && $seqcount == @seqs; next; } if (/^\s*(\d+)\s+(\d+)\s+$/) { $seqcount = $1; next } # runmode = (0) # this should in fact be packed into a Bio::SimpleAlign object # instead of an array but we'll stay with this for now if (/^node/) { my ( $name, $num, $seqstr ) = split( /\s+/, $_, 3 ); $name .= $num; $seqstr =~ s/\s+//g; # remove whitespace unless (@firstseq) { @firstseq = split( //, $seqstr ); push @seqs, Bio::LocatableSeq->new( -display_id => $name, -seq => $seqstr ); } else { my $i = 0; my $v; while ( ( $v = index( $seqstr, '.', $i ) ) >= $i ) { # replace the '.' with the correct seq from the substr( $seqstr, $v, 1, $firstseq[$v] ); $i = $v; } $self->debug("adding seq $seqstr\n"); push @seqs, Bio::LocatableSeq->new( -display_id => $name, -seq => $seqstr ); } } } $self->{'_rst'}->{'rctrted_seqs'} = \@seqs; } else { } } $self->{'_rst'}->{'trees'} = \@trees; return; } 1; __END__ =pod =encoding UTF-8 =head1 NAME Bio::Tools::Phylo::PAML - Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00 =head1 VERSION version 1.7.3 =head1 SYNOPSIS #!/usr/bin/perl -Tw use strict; use Bio::Tools::Phylo::PAML; # need to specify the output file name (or a fh) (defaults to # -file => "codeml.mlc"); also, optionally, the directory in which # the other result files (rst, 2ML.dS, etc) may be found (defaults # to "./") my $parser = Bio::Tools::Phylo::PAML->new (-file => "./results/mlc", -dir => "./results/"); # get the first/next result; a Bio::Tools::Phylo::PAML::Result object, # which isa Bio::SeqAnalysisResultI object. my $result = $parser->next_result(); # get the sequences used in the analysis; returns Bio::PrimarySeq # objects (OTU = Operational Taxonomic Unit). my @otus = $result->get_seqs(); # codon summary: codon usage of each sequence [ arrayref of { # hashref of counts for each codon } for each sequence and the # overall sum ], and positional nucleotide distribution [ arrayref # of { hashref of frequencies for each nucleotide } for each # sequence and overall frequencies ]: my ($codonusage, $ntdist) = $result->get_codon_summary(); # example manipulations of $codonusage and $ntdist: printf "There were %d %s codons in the first seq (%s)\n", $codonusage->[0]->{AAA}, 'AAA', $otus[0]->id(); printf "There were %d %s codons used in all the sequences\n", $codonusage->[$#{$codonusage}]->{AAA}, 'AAA'; printf "Nucleotide %c was present %g of the time in seq %s\n", 'A', $ntdist->[1]->{A}, $otus[1]->id(); # get Nei & Gojobori dN/dS matrix: my $NGmatrix = $result->get_NGmatrix(); # get ML-estimated dN/dS matrix, if calculated; this corresponds to # the runmode = -2, pairwise comparison usage of codeml my $MLmatrix = $result->get_MLmatrix(); # These matrices are length(@otu) x length(@otu) "strict lower # triangle" 2D-matrices, which means that the diagonal and # everything above it is undefined. Each of the defined cells is a # hashref of estimates for "dN", "dS", "omega" (dN/dS ratio), "t", # "S" and "N". If a ML matrix, "lnL" and "kappa" will also be defined. printf "The omega ratio for sequences %s vs %s was: %g\n", $otus[0]->id, $otus[1]->id, $MLmatrix->[0]->[1]->{omega}; # with a little work, these matrices could also be passed to # Bio::Tools::Run::Phylip::Neighbor, or other similar tree-building # method that accepts a matrix of "distances" (using the LOWTRI # option): my $distmat = [ map { [ map { $$_{omega} } @$_ ] } @$MLmatrix ]; # for runmode's other than -2, get tree topology with estimated # branch lengths; returns a Bio::Tree::TreeI-based tree object with # added PAML parameters at each node my ($tree) = $result->get_trees(); for my $node ($tree->get_nodes()) { # inspect the tree: the "t" (time) parameter is available via # $node->branch_length(); all other branch-specific parameters # ("omega", "dN", etc.) are available via # ($omega) = $node->get_tag_values('omega'); } # if you are using model based Codeml then trees are stored in each # modelresult object for my $modelresult ( $result->get_NSSite_results ) { # model M0, M1, etc print "model is ", $modelresult->model_num, "\n"; my ($tree) = $modelresult->get_trees(); for my $node ($tree->get_nodes()) { # inspect the tree: the "t" (time) parameter is available via # $node->branch_length(); all other branch-specific parameters # ("omega", "dN", etc.) are available via # ($omega) = $node->get_tag_values('omega'); } } # get any general model parameters: kappa (the # transition/transversion ratio), NSsites model parameters ("p0", # "p1", "w0", "w1", etc.), etc. my $params = $result->get_model_params(); printf "M1 params: p0 = %g\tp1 = %g\n", $params->{p0}, $params->{p1}; # parse AAML result files my $aamat = $result->get_AADistMatrix(); my $aaMLmat = $result->get_AAMLDistMatrix(); =head1 DESCRIPTION This module is used to parse the output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio::Tools::Run::Phylo::PAML::* modules to actually run some of the PAML programs, but this module is only useful to parse the output. This module has fledgling support for PAML version 4.3a (October 2009). Please report any problems to the mailing list (see FEEDBACK below). =head2 parse_codeml example use Bio::Tools::Phylo::PAML; my $parser = new Bio::Tools::Phylo::PAML(-file => shift, -verbose => shift); my $result = $parser->next_result; my @otus = $result->get_seqs(); my $MLmatrix = $result->get_MLmatrix(); my $NGmatrix = $result->get_NGmatrix(); # These matrices are length(@otu) x length(@otu) "strict lower # triangle" 2D-matrices, which means that the diagonal and # everything above it is undefined. Each of the defined cells is a # hashref of estimates for "dN", "dS", "omega" (dN/dS ratio), "t", # "S" and "N". If a ML matrix, "lnL" will also be defined. @otus = $result->get_seqs(); $MLmatrix = $result->get_MLmatrix(); $NGmatrix = $result->get_NGmatrix(); for( my $i=0;$i[$i]}; $j++ ) { printf "The ML omega ratio for sequences %s vs %s was: %g\n", $otus[$i]->id, $otus[$j]->id, $MLmatrix->[$i]->[$j]->{omega}; } } for( my $i=0;$i[$i]}; $j++ ) { printf "The NG omega ratio for sequences %s vs %s was: %g\n", $otus[$i]->id, $otus[$j]->id, $NGmatrix->[$i]->[$j]->{'omega'}; } } =head1 METHODS =head2 new Title : new Usage : my $obj = Bio::Tools::Phylo::PAML->new(%args); Function: Builds a new Bio::Tools::Phylo::PAML object Returns : Bio::Tools::Phylo::PAML Args : Hash of options: -file, -fh, -dir -file (or -fh) should contain the contents of the PAML outfile; -dir is the (optional) name of the directory in which the PAML program was run (and includes other PAML-generated files from which we can try to gather data) =head2 Implement Bio::AnalysisParserI interface =head2 next_result Title : next_result Usage : $result = $obj->next_result(); Function: Returns the next result available from the input, or undef if there are no more results. Example : Returns : a Bio::Tools::Phylo::PAML::Result object Args : none =head1 TO DO Implement get_posteriors(). For NSsites models, obtain arrayrefs of posterior probabilities for membership in each class for every position; probabilities correspond to classes w0, w1, ... etc. my @probs = $result->get_posteriors(); # find, say, positively selected sites! if ($params->{w2} > 1) { for (my $i = 0; $i < @probs ; $i++) { if ($probs[$i]->[2] > 0.5) { # assumes model M1: three w's, w0, w1 and w2 (positive selection) printf "position %d: (%g prob, %g omega, %g mean w)\n", $i, $probs[$i]->[2], $params->{w2}, $probs[$i]->[3]; } } } else { print "No positive selection found!\n"; } =head1 TODO RST parsing -- done, Avilella contributions bug#1506, added by jason 1.29 -- still need to parse in joint probability and non-syn changes at site table =head1 FEEDBACK =head2 Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bio-tools-phylo-paml/issues =head1 AUTHORS Jason Stajich Aaron Mackey Albert Vilella Sendu Bala Dave Messina =head1 COPYRIGHT This software is copyright (c) by Jason Stajich , and by Aaron Mackey . This software is available under the same terms as the perl 5 programming language system itself. =cut Bio-Tools-Phylo-PAML-1.7.3/lib/Bio/Tools/Run/0000755000175000017500000000000013316145226021277 5ustar carandraugcarandraugBio-Tools-Phylo-PAML-1.7.3/lib/Bio/Tools/Run/Phylo/0000755000175000017500000000000013316145226022372 5ustar carandraugcarandraugBio-Tools-Phylo-PAML-1.7.3/lib/Bio/Tools/Run/Phylo/PAML/0000755000175000017500000000000013316145226023123 5ustar carandraugcarandraugBio-Tools-Phylo-PAML-1.7.3/lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm0000644000175000017500000006450213316145226024673 0ustar carandraugcarandraugpackage Bio::Tools::Run::Phylo::PAML::Codeml; $Bio::Tools::Run::Phylo::PAML::Codeml::VERSION = '1.7.3'; use utf8; use strict; use warnings; use vars qw(@ISA %VALIDVALUES $MINNAMELEN $PROGRAMNAME $PROGRAM); use Bio::Root::Root; use Bio::AlignIO; use Bio::TreeIO; use Bio::Tools::Run::WrapperBase; use Bio::Tools::Phylo::PAML; use Cwd; @ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase); # ABSTRACT: Wrapper aroud the PAML program codeml # AUTHOR: Jason Stajich # OWNER: Jason Stajich # LICENSE: Perl_5 BEGIN { $MINNAMELEN = 25; $PROGRAMNAME = 'codeml' . ($^O =~ /mswin/i ?'.exe':''); if( defined $ENV{'PAMLDIR'} ) { $PROGRAM = Bio::Root::IO->catfile($ENV{'PAMLDIR'},$PROGRAMNAME). ($^O =~ /mswin/i ?'.exe':'');; } # valid values for parameters, the default one is always # the first one in the array # much of the documentation here is lifted directly from the codeml.ctl # example file provided with the package %VALIDVALUES = ( 'outfile' => 'mlc', 'noisy' => [ 0..3,9], 'verbose' => [ 1,0,2], # 0:concise, 1:detailed, 2:too much # (runmode) 0:user tree, 1:semi-autmatic, 2:automatic # 3:stepwise addition, 4,5:PerturbationNNI # -2:pairwise 'runmode' => [ -2, 0..5], 'seqtype' => [ 1..3], # 1:codons, 2:AAs, 3:codons->AAs 'CodonFreq' => [ 2, 0,1,3,4,5,6,7], # 0:1/61 each, 1:F1X4, # 2:F3X4, 3:codon table # (aaDist) 0:equal, +:geometric, -:linear, # 1-6:G1974,Miyata, c,p,v,a 'aaDist' => [ 0,'+','-', 1..6], # (aaRatefile) only used for aa seqs # with model=empirical(_F) # default is usually 'wag.dat', also # dayhoff.dat, jones.dat, mtmam.dat, or your own 'aaRatefile' => 'wag.dat', # (model) models for codons # 0: one, 1:b, 2:2 or more dN/dS ratios for branches 'model' => [0..3,7], # (NSsites) number of S sites # 0: one w;1:neutral;2:selection; 3:discrete;4:freqs; # 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ # 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1; # 13:3normal>0 'NSsites' => [0..13], # (icode) genetic code # 0:universal code # 1:mamalian mt # 2:yeast mt # 3:mold mt, # 4:invertebrate mt # 5:ciliate nuclear # 6:echinoderm mt # 7:euplotid mt # 8:alternative yeast nu. # 9:ascidian mt #10:blepharisma nu # these correspond to 1-11 in the genbank transl table 'icode' => [ 0..10], 'Mgene' => [0,1], # 0:rates, 1:separate 'fix_kappa'=> [0,1], # 0:estimate kappa, 1:fix kappa 'kappa' => '2', # initial or fixed kappa 'fix_omega'=> [0,1], # 0: estimate omega, 1: fix omega 'omega' => '1', # initial or fixed omega for # codons or codon-base AAs 'fix_alpha'=> [1,0], # 0: estimate gamma shape param # 1: fix it at alpha 'alpha' => '0.', # initial or fixed alpha # 0: infinity (constant rate) 'Malpha' => [0,1], # different alphas for genes 'ncatG' => [1..10], # number of categories in # dG of NSsites models # (clock) # 0: no clock, 1: global clock, 2: local clock # 3: TipDate 'clock' => [0..3], # (getSE) Standard Error: # 0:don't want them, 1: want S.E. 'getSE' => [0,1], # (RateAncestor) # 0,1,2 rates (alpha>0) or # ancestral states (1 or 2) 'RateAncestor' => [1,0,2], 'Small_Diff' => '.5e-6', # (cleandata) remove sites with ambiguity data # 1: yes, 0:no 'cleandata' => [0,1], # this is the number of datasets in # the file - we would need to change # our api to allow >1 alignment object # to be referenced at time 'ndata' => 1, # (method) # 0: simultaneous,1: 1 branch at a time 'method' => [0,1], # allow branch lengths to be fixed # 0 ignore # -1 use random starting points # 1 use the branch lengths in initial ML iteration # 2 branch lengths are fixed 'fix_blength' => [0,-1,1,2], ); } sub program_name { return 'codeml'; } sub program_dir { return Bio::Root::IO->catfile($ENV{PAMLDIR}) if $ENV{PAMLDIR}; } sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_branchLengths'} = 0; my ($aln, $tree, $st, $params, $exe, $ubl) = $self->_rearrange([qw(ALIGNMENT TREE SAVE_TEMPFILES PARAMS EXECUTABLE BRANCHLENGTHS)], @args); defined $aln && $self->alignment($aln); defined $tree && $self->tree($tree, branchLengths => ($ubl || 0) ); defined $st && $self->save_tempfiles($st); defined $exe && $self->executable($exe); $self->set_default_parameters(); if( defined $params ) { if( ref($params) !~ /HASH/i ) { $self->warn("Must provide a valid hash ref for parameter -FLAGS"); } else { map { $self->set_parameter($_, $$params{$_}) } keys %$params; } } return $self; } sub prepare{ my ($self,$aln,$tree) = @_; unless ( $self->save_tempfiles ) { # brush so we don't get plaque buildup ;) $self->cleanup(); } $tree = $self->tree unless $tree; $aln = $self->alignment unless $aln; if( ! $aln ) { $self->warn("must have supplied a valid alignment file in order to run codeml"); return 0; } my ($tempdir) = $self->tempdir(); my ($tempseqFH,$tempseqfile); if( ! ref($aln) && -e $aln ) { $tempseqfile = $aln; } else { ($tempseqFH,$tempseqfile) = $self->io->tempfile ('-dir' => $tempdir, UNLINK => ($self->save_tempfiles ? 0 : 1)); my $alnout = Bio::AlignIO->new('-format' => 'phylip', '-fh' => $tempseqFH, '-interleaved' => 0, '-idlength' => $MINNAMELEN > $aln->maxdisplayname_length() ? $MINNAMELEN : $aln->maxdisplayname_length() +1); $alnout->write_aln($aln); $alnout->close(); undef $alnout; close($tempseqFH); } # now let's print the codeml.ctl file. # many of the these programs are finicky about what the filename is # and won't even run without the properly named file. Ack my $codeml_ctl = "$tempdir/codeml.ctl"; open(CODEML, ">$codeml_ctl") or $self->throw("cannot open $codeml_ctl for writing"); print CODEML "seqfile = $tempseqfile\n"; my $outfile = $self->outfile_name; print CODEML "outfile = $outfile\n"; if( $tree ) { my ($temptreeFH,$temptreefile); if( ! ref($tree) && -e $tree ) { $temptreefile = $tree; } else { ($temptreeFH,$temptreefile) = $self->io->tempfile ('-dir' => $tempdir, UNLINK => ($self->save_tempfiles ? 0 : 1)); my $treeout = Bio::TreeIO->new('-format' => 'newick', '-fh' => $temptreeFH); $treeout->write_tree($tree); $treeout->close(); close($temptreeFH); } print CODEML "treefile = $temptreefile\n"; } my %params = $self->get_parameters; while( my ($param,$val) = each %params ) { next if $param eq 'outfile'; print CODEML "$param = $val\n"; } close(CODEML); # my ($rc,$parser) = (1); # { # my $cwd = cwd(); # my $exit_status; # chdir($tempdir); # } return $tempdir; } sub run { my ($self) = shift;; my $outfile = $self->outfile_name; my $tmpdir = $self->prepare(@_); my ($rc,$parser) = (1); { my $cwd = cwd(); my $exit_status; chdir($tmpdir); my $codemlexe = $self->executable(); $self->throw("unable to find or run executable for 'codeml'") unless $codemlexe && -e $codemlexe && -x _; my $run; if( $self->{'_branchLengths'} ) { open($run, "echo $self->{'_branchLengths'} | $codemlexe |") or $self->throw("Cannot open exe $codemlexe"); } else { open($run, "$codemlexe |") or $self->throw("Cannot open exe $codemlexe"); } my @output = <$run>; $exit_status = close($run); $self->error_string(join('',@output)); if( (grep { /\berr(or)?: /io } @output) || !$exit_status) { $self->warn("There was an error - see error_string for the program output"); $rc = 0; } eval { $parser = Bio::Tools::Phylo::PAML->new(-file => "$tmpdir/$outfile", -verbose => $self->verbose, -dir => "$tmpdir"); }; if( $@ ) { $self->warn($self->error_string); } chdir($cwd); } return ($rc,$parser); } sub error_string{ my ($self,$value) = @_; if( defined $value) { $self->{'error_string'} = $value; } return $self->{'error_string'}; } sub alignment{ my ($self,$aln) = @_; if( defined $aln ) { if( -e $aln ) { $self->{'_alignment'} = $aln; } elsif( !ref($aln) || ! $aln->isa('Bio::Align::AlignI') ) { $self->warn("Must specify a valid Bio::Align::AlignI object to the alignment function not $aln"); return undef; } else { $self->{'_alignment'} = $aln; } } return $self->{'_alignment'}; } sub tree { my ($self, $tree, %params) = @_; if( defined $tree ) { if( ! ref($tree) || ! $tree->isa('Bio::Tree::TreeI') ) { $self->warn("Must specify a valid Bio::Tree::TreeI object to the alignment function"); } $self->{'_tree'} = $tree; if ( defined $params{'_branchLengths'} ) { my $ubl = $params{'_branchLengths'}; if ($ubl !~ m/^(0|1|2)$/) { $self->throw("The branchLengths parameter to tree() must be 0 (ignore), 1 (initial values) or 2 (fixed values) only"); } $self->{'_branchLengths'} = $ubl; } } return $self->{'_tree'}; } sub get_parameters{ my ($self) = @_; # we're returning a copy of this return %{ $self->{'_codemlparams'} }; } sub set_parameter{ my ($self,$param,$value) = @_; unless (defined $self->{'no_param_checks'} && $self->{'no_param_checks'} == 1) { if ( ! defined $VALIDVALUES{$param} ) { $self->warn("unknown parameter $param will not be set unless you force by setting no_param_checks to true"); return 0; } if ( ref( $VALIDVALUES{$param}) =~ /ARRAY/i && scalar @{$VALIDVALUES{$param}} > 0 ) { unless ( grep { $value eq $_ } @{ $VALIDVALUES{$param} } ) { $self->warn("parameter $param specified value $value is not recognized, please see the documentation and the code for this module or set the no_param_checks to a true value"); return 0; } } } $self->{'_codemlparams'}->{$param} = $value; return 1; } sub set_default_parameters{ my ($self,$keepold) = @_; $keepold = 0 unless defined $keepold; while( my ($param,$val) = each %VALIDVALUES ) { # skip if we want to keep old values and it is already set next if( defined $self->{'_codemlparams'}->{$param} && $keepold); if(ref($val)=~/ARRAY/i ) { $self->{'_codemlparams'}->{$param} = $val->[0]; } else { $self->{'_codemlparams'}->{$param} = $val; } } } sub no_param_checks{ my ($self,$value) = @_; if( defined $value) { $self->{'no_param_checks'} = $value; } return $self->{'no_param_checks'}; } sub outfile_name { my $self = shift; if( @_ ) { return $self->{'_codemlparams'}->{'outfile'} = shift @_; } unless (defined $self->{'_codemlparams'}->{'outfile'}) { $self->{'_codemlparams'}->{'outfile'} = 'mlc'; } return $self->{'_codemlparams'}->{'outfile'}; } sub DESTROY { my $self= shift; unless ( $self->save_tempfiles ) { $self->cleanup(); } $self->SUPER::DESTROY(); } 1; __END__ =pod =encoding UTF-8 =head1 NAME Bio::Tools::Run::Phylo::PAML::Codeml - Wrapper aroud the PAML program codeml =head1 VERSION version 1.7.3 =head1 SYNOPSIS use Bio::Tools::Run::Phylo::PAML::Codeml; use Bio::AlignIO; my $alignio = Bio::AlignIO->new(-format => 'phylip', -file => 't/data/gf-s85.phylip'); my $aln = $alignio->next_aln; my $codeml = Bio::Tools::Run::Phylo::PAML::Codeml->new(); $codeml->alignment($aln); my ($rc,$parser) = $codeml->run(); my $result = $parser->next_result; my $MLmatrix = $result->get_MLmatrix(); print "Ka = ", $MLmatrix->[0]->[1]->{'dN'},"\n"; print "Ks = ", $MLmatrix->[0]->[1]->{'dS'},"\n"; print "Ka/Ks = ", $MLmatrix->[0]->[1]->{'omega'},"\n"; =head1 DESCRIPTION This is a wrapper around the codeml program of PAML (Phylogenetic Analysis by Maximum Likelihood) package of Ziheng Yang. See http://abacus.gene.ucl.ac.uk/software/paml.html for more information. This module is more about generating the properl codeml.ctl file and will run the program in a separate temporary directory to avoid creating temp files all over the place. =head2 Default Values Valid and default values for codeml programs are listed below. The default values are always the first one listed. These descriptions are essentially lifted from the example codeml.ctl file and pamlDOC documentation provided by the author. B specifies the equilibrium codon frequencies in codon substitution model. These frequencies can be assumed to be equal (1/61 each for the standard genetic code, B = 0), calculated from the average nucleotide frequencies (B = 1), from the average nucleotide frequencies at the three codon positions (B = 2), or used as free parameters (B = 3). The number of parameters involved in those models of codon frequencies is 0, 3, 9, and 60 (under the universal code), for B = 0, 1, 2, and 3 respectively. B specifies whether equal amino acid distances are assumed (= 0) or Grantham's matrix is used (= 1) (Yang et al. 1998). B = -2 performs ML estimation of dS and dN in pairwise comparisons. The program will collect estimates of dS and dN into the files 2ML.dS and 2ML.dN. Since many users seem interested in looking at dN /dS ratios among lineages, examination of the tree shapes indicated by branch lengths calculated from the two rates may be interesting although the analysis is ad hoc. If your species names have no more than 10 characters, you can use the output distance matrices as input to Phylip programs such as neighbor without change. Otherwise you need to edit the files to cut the names short. B concerns assumptions about the dN/dS rate ratios among branches (Yang 1998; Yang and Nielsen 1998). B =0 means a single dN/dS ratio for all lineages (branches), 1 means one ratio for each branch (free ratio model), and 2 means arbitrary number of rations (such as the 2-ratios or 3-ratios models. with B =2, you may specify the omega ratios for the branches using branch labels (read about the tree structure file in the document). This option seems rather easy to use. Otherwise, the program will ask the user to input a branch mark for the dN/dS ratio assumed for each branch. This should be an integral number between 0 to k - 1 if k different dN/dS ratios (omega_0 - omega_k - 1) are assumed for the branches of the tree. B note basically, doing this interactively is not going to work very well, so this module is really focused around using the 0 or 1 parameters. Read the program documentation if you'd like some more detailed instructions. B specifies models that allow the dN/dS ratio (omega) to vary among sites (Nielsen and Yang 1998, Yang et al. 2000) B = m corresponds to model Mm in Yang et al (2000). The variable B is used to specify the number of categories in the omega distribution under some models. The values of ncatG() used to perform our analyses are 3 for M3 (discrete), 5 for M4 (freq), 10 for the continuous distributions (M5: gamma, M6: 2gamma, M7: beta, M8:beta&w, M9:beta&gamma, M10: beta&gamma+1, M11:beta&normal>1, and M12:0&2normal>1, M13:3normal>0). This means M8 will have 11 site classes (10 from the beta distribution plus 1 additional class). The posterior probabilities for site classes as well as the expected omega values for sites are listed in the file rst, which may be useful to pinpoint sites under positive selection, if they exist. To make it easy to run several B models in one go, the executable L can be used, which asks you how many and which models to run at the start of the program. The number of categories used will then match those used in Yang et al(2000). As noted in that paper, some of the models are hard to use, in particular, M12 and M13. Recommended models are 0 (one-ratio), 1 (neutral), 2 (selection), 3 (discrete), 7 (beta), and 8 (beta&omega ). Some of the models like M2 and M8 are noted to be prone to the problem of multiple local optima. You are advised to run the program at least twice, once with a starting omega value E1 and a second time with a value E1, and use the results corresponding to the highest likelihood. The continuous neutral and selection models of Nielsen and Yang (1998) are not implemented in the program. B for genetic code and these correspond to 1-11 in the genbank transl table. 0:universal code 1:mamalian mt 2:yeast mt 3:mold mt, 4:invertebrate mt 5:ciliate nuclear 6:echinoderm mt 7:euplotid mt 8:alternative yeast nu. 9:ascidian mt 10:blepharisma nu B For codon sequences, ancestral reconstruction is not implemented for the models of variable dN/dS ratios among sites. The output under codon-based models usually shows the encoded amino acid for each codon. The output under "Prob of best character at each node, listed by site" has two posterior probabilities for each node at each codon (amino acid) site. The first is for the best codon. The second, in parentheses, is for the most likely amino acid under the codon substitution model. This is a sum of posterior probabilities across synonymous codons. In theory it is possible although rare for the most likely amino acid not to match the most likely codon. B for codon sequences (seqtype = 1): The codon frequencies in each sequence are counted and listed in a genetic code table, together with their sums across species. Each table contains six or fewer species. For data of multiple genes (option G in the sequence file), codon frequencies in each gene (summed over species) are also listed. The nucleotide distributions at the three codon positions are also listed. The method of Nei and Gojobori (1986) is used to calculate the number of synonymous substitutions per synonymous site (dS ) and the number of nonsynonymous substitutions per nonsynonymous site (dN ) and their ratio (dN /dS ). These are used to construct initial estimates of branch lengths for the likelihood analysis but are not MLEs themselves. Note that the estimates of these quantities for the a- and b-globin genes shown in Table 2 of Goldman and Yang (1994), calculated using the MEGA package (Kumar et al., 1993), are not accurate. Results of ancestral reconstructions (B = 1) are collected in the file rst. Under models of variable dN/dS ratios among sites (NSsites models), the posterior probabilities for site classes as well as positively selected sites are listed in rst. INCOMPLETE DOCUMENTATION OF ALL METHODS =head1 ATTRIBUTES =head2 program_name Title : program_name Usage : $factory->program_name() Function: holds the program name Returns: string Args : None =head2 program_dir Title : program_dir Usage : ->program_dir() Function: returns the program directory, obtained from ENV variable. Returns: string Args : =head2 error_string Title : error_string Usage : $obj->error_string($newval) Function: Where the output from the last analysus run is stored. Returns : value of error_string Args : newvalue (optional) =head2 alignment Title : alignment Usage : $codeml->align($aln); Function: Get/Set the L object Returns : L object Args : [optional] L Comment : We could potentially add support for running directly on a file but we shall keep it simple See also: L =head2 tree Title : tree Usage : $codeml->tree($tree, %params); Function: Get/Set the L object Returns : L Args : [optional] $tree => L, [optional] %parameters => hash of tree-specific parameters: branchLengths: 0, 1 or 2 out Comment : We could potentially add support for running directly on a file but we shall keep it simple See also: L =head2 no_param_checks Title : no_param_checks Usage : $obj->no_param_checks($newval) Function: Boolean flag as to whether or not we should trust the sanity checks for parameter values Returns : value of no_param_checks Args : newvalue (optional) =head2 save_tempfiles Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional) =head2 outfile_name Title : outfile_name Usage : my $outfile = $codeml->outfile_name(); Function: Get/Set the name of the output file for this run (if you wanted to do something special) Returns : string Args : [optional] string to set value to =head2 tempdir Title : tempdir Usage : my $tmpdir = $self->tempdir(); Function: Retrieve a temporary directory name (which is created) Returns : string which is the name of the temporary directory Args : none =head1 METHODS =head2 new Title : new Usage : my $obj = Bio::Tools::Run::Phylo::PAML::Codeml->new(); Function: Builds a new Bio::Tools::Run::Phylo::PAML::Codeml object Returns : Bio::Tools::Run::Phylo::PAML::Codeml Args : -alignment => the Bio::Align::AlignI object -save_tempfiles => boolean to save the generated tempfiles and NOT cleanup after onesself (default FALSE) -tree => the Bio::Tree::TreeI object -branchlengths => 0: ignore any branch lengths found on the tree 1: use as initial values 2: fix branch lengths -params => a hashref of PAML parameters (all passed to set_parameter) -executable => where the codeml executable resides See also: L, L =head2 prepare Title : prepare Usage : my $rundir = $codeml->prepare($aln); Function: prepare the codeml analysis using the default or updated parameters the alignment parameter must have been set Returns : value of rundir Args : L object, L object [optional] =head2 run Title : run Usage : my ($rc,$parser) = $codeml->run($aln,$tree); Function: run the codeml analysis using the default or updated parameters the alignment parameter must have been set Returns : Return code, L Args : L object, L object [optional] =head2 get_parameters Title : get_parameters Usage : my %params = $self->get_parameters(); Function: returns the list of parameters as a hash Returns : associative array keyed on parameter names Args : none =head2 set_parameter Title : set_parameter Usage : $codeml->set_parameter($param,$val); Function: Sets a codeml parameter, will be validated against the valid values as set in the %VALIDVALUES class variable. The checks can be ignored if one turns off param checks like this: $codeml->no_param_checks(1) Returns : boolean if set was success, if verbose is set to -1 then no warning will be reported Args : $param => name of the parameter $value => value to set the parameter to See also: L =head2 set_default_parameters Title : set_default_parameters Usage : $codeml->set_default_parameters(0); Function: (Re)set the default parameters from the defaults (the first value in each array in the %VALIDVALUES class variable) Returns : none Args : boolean: keep existing parameter values =head2 cleanup Title : cleanup Usage : $codeml->cleanup(); Function: Will cleanup the tempdir directory after a PAML run Returns : none Args : none =head2 io Title : io Usage : $obj->io($newval) Function: Gets a L object Returns : L Args : none =head1 Bio::Tools::Run::WrapperBase methods =head1 FEEDBACK =head2 Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bio-tools-phylo-paml/issues =head1 AUTHOR Jason Stajich =head1 COPYRIGHT This software is copyright (c) by Jason Stajich . This software is available under the same terms as the perl 5 programming language system itself. =cut Bio-Tools-Phylo-PAML-1.7.3/lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm0000644000175000017500000005251313316145226025111 0ustar carandraugcarandraugpackage Bio::Tools::Run::Phylo::PAML::Evolver; $Bio::Tools::Run::Phylo::PAML::Evolver::VERSION = '1.7.3'; use utf8; use strict; use warnings; use vars qw(@ISA %VALIDVALUES $MINNAMELEN $PROGRAMNAME $PROGRAM); use Bio::Root::Root; use Bio::AlignIO; use Bio::SeqIO; use Bio::TreeIO; use Bio::Tools::Run::WrapperBase; use Bio::Tools::Phylo::PAML; use Cwd; @ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase); # ABSTRACT: Wrapper aroud the PAML program evolver # AUTHOR: Albert Vilella # OWNER: Albert Vilella # LICENSE: Perl_5 BEGIN { $MINNAMELEN = 25; $PROGRAMNAME = 'evolver' . ($^O =~ /mswin/i ?'.exe':''); if( defined $ENV{'PAMLDIR'} ) { $PROGRAM = Bio::Root::IO->catfile($ENV{'PAMLDIR'},$PROGRAMNAME). ($^O =~ /mswin/i ?'.exe':'');; } # valid values for parameters, the default one is always # the first one in the array # much of the documentation here is lifted directly from the MCcodon.dat # example file provided with the package # Evolver calls time for seed: SetSeed(i==-1?(int)time(NULL):i); my $rand = int(time); # my $rand = int(rand(999999)); %VALIDVALUES = ( # FIXME: there should be a 6-7-8 option that fits MCcodon or MCbase or MCaa 'outfmt' => [0,1], # 0 * 0:paml format (mc.paml); 1:paup format (mc.paup) # random number seed (odd number) # FIXME: set seed to null here and ask for it later? 'seed' => "$rand", # numseq can actually be calculated from the tree external nodes # nucleotide sites 'nuclsites' => '1000', # replicates 'replicates' => '1', # tree length; use -1 if tree has absolute branch lengths # Note that tree length and branch lengths under the codon model are # measured by the expected number of nucleotide substitutions per codon # (see Goldman & Yang 1994). For amino acid models, they are defined as # the expected number of amino acid changes per amino acid site. 'tree_length' => '1.5', # omega # FIXME: if one wants to call for different omegas (NSsites), # right now it has to be done like: # $evolver->set_parameter(omega,"3\n0.2\t0.3\t0.5\n0.5\t0.9\t3.2\n"); # 3 * number of site classes, followed by frequencies and omega's. # 0.6 0.3 0.1 # Freqs # 0.1 0.8 3.2 # Omegas 'omega' => '0.3', # kappa 'kappa' => '5', # FIXME: this only for MCbase.dat ? # model: 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85, 5:T92, 6:TN93, 7:REV # FIXME: this applies to only some models? # 10 5 1 2 3 * kappa or rate parameters in model # FIXME: this applies to only MCbase.dat ? # 0.5 4 * <#categories for discrete gamma> ); # end of validvalues } sub program_name { return 'evolver'; } sub program_dir { return Bio::Root::IO->catfile($ENV{PAMLDIR}) if $ENV{PAMLDIR}; } sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); # $self->{'_branchLengths'} = 0; my ($tree, $st, $params, $exe) = $self->_rearrange([qw(TREE SAVE_TEMPFILES PARAMS EXECUTABLE)], @args); defined $tree && $self->tree($tree); defined $st && $self->save_tempfiles($st); defined $exe && $self->executable($exe); $self->set_default_parameters(); if( defined $params ) { if( ref($params) !~ /HASH/i ) { $self->warn("Must provide a valid hash ref for parameter -FLAGS"); } else { map { $self->set_parameter($_, $$params{$_}) } keys %$params; } } return $self; } sub prepare { my ($self,$aln,$tree) = @_; # FIXME: To consider: to have save_tempfiles always TRUE by default # or simply never delete unless ( $self->save_tempfiles ) { # brush so we don't get plaque buildup ;) $self->cleanup(); } $tree = $self->tree unless $tree; my ($tempdir) = $self->tempdir(); # FIXME: # If multiple replicates, evolver gives: # A file with a concatenation of sequential phylips separated by a # double return which gets correctly parsed by AlignIO next_aln # Or a concatenation of paup entries with tags separating them which # wont get correctly parsed with current AlignIO (failed with # nexus) # FIXME: To consider: force phylip outfmt and split the files if # replicates > 1 # if( ! ref($aln) && -e $aln ) { # $tempseqfile = $aln; # } else { # ($tempseqFH,$tempseqfile) = $self->io->tempfile # ('-dir' => $tempdir, # UNLINK => ($self->save_tempfiles ? 0 : 1)); # my $alnout = Bio::AlignIO->new('-format' => 'phylip', # '-fh' => $tempseqFH, # '-interleaved' => 0, # '-idlength' => $MINNAMELEN > $aln->maxdisplayname_length() ? $MINNAMELEN : $aln->maxdisplayname_length() +1); # $alnout->write_aln($aln); # $alnout->close(); # undef $alnout; # close($tempseqFH); # } # now let's print the MCcodon.dat file. # many of the these programs are finicky about what the filename is # and won't even run without the properly named file. Ack # FIXME: we should do the appropriate here if we are simulating codons, nts o aa. my $evolver_ctl = "$tempdir/MCcodon.dat"; my $evolverfh; open($evolverfh, ">$evolver_ctl") or $self->throw("cannot open $evolver_ctl for writing"); # FIXME: params follow an order in the control file, they are not a hash. Do we have an # clean example of this in bioperl-run? my %params = $self->get_parameters; print $evolverfh "$params{outfmt}\n"; print $evolverfh "$params{seed}\n"; # FIXME: call get_leaf_nodes to count only leafs - relates to newick onlyleafids bug # my $numseq = scalar($tree->get_nodes); my $numseq = scalar($tree->get_leaf_nodes); print $evolverfh "$numseq "; print $evolverfh "$params{nuclsites} "; print $evolverfh "$params{replicates}\n\n"; print $evolverfh "$params{tree_length}\n"; # FIXME: do #1:#n branch tagging magic here # FIXME: this pre flush stuff is for appending mode my $treeout = Bio::TreeIO->new ('-format' => 'newick', '-fh' => $evolverfh, -PRE =>'>>', '-flush', ); # $treeout->bootstrap_style('nointernalids'); $treeout->write_tree($tree); # Appending mode to add more control file contents here open($evolverfh, ">>$evolver_ctl") or $self->throw("cannot open $evolver_ctl for writing"); print $evolverfh "\n$params{omega}\n"; print $evolverfh "$params{kappa}\n"; # Print codon freqs here or defaults (below) my @codon_freqs = $self->get_CodonFreqs(); foreach my $firstbase (@codon_freqs) { foreach my $element (@$firstbase) { print $evolverfh " $element"; } print $evolverfh "\n"; } # FIXME: codon freqs or nt freqs should always come from an object? # Silly printing the default codonfreqs in the default # MCcodon.dat provided by PAML unless (@codon_freqs) { print $evolverfh "0.00983798 0.01745548 0.00222048 0.01443315\n", "0.00844604 0.01498576 0.00190632 0.01239105\n", "0.01064012 0.01887870 0 0\n", "0.00469486 0.00833007 0 0.00688776\n", "0.01592816 0.02826125 0.00359507 0.02336796\n", "0.01367453 0.02426265 0.00308642 0.02006170\n", "0.01722686 0.03056552 0.00388819 0.02527326\n", "0.00760121 0.01348678 0.00171563 0.01115161\n", "0.01574077 0.02792876 0.00355278 0.02309304\n", "0.01351366 0.02397721 0.00305010 0.01982568\n", "0.01702419 0.03020593 0.00384245 0.02497593\n", "0.00751178 0.01332811 0.00169545 0.01102042\n", "0.02525082 0.04480239 0.00569924 0.03704508\n", "0.02167816 0.03846344 0.00489288 0.03180369\n", "0.02730964 0.04845534 0.00616393 0.04006555\n", "0.01205015 0.02138052 0.00271978 0.01767859\n"; } print $evolverfh "\n// end of file.\n"; close($evolverfh); # FIXME: what do we return in prepare? # return } sub run { my $self = shift; # FIXME: We should look for the stuff we prepared in the prepare method here my $rc = (1); { my $exit_status; my ($tmpdir) = $self->tempdir(); chdir($tmpdir); my $evolverexe = $self->executable(); $self->throw("unable to find or run executable for 'evolver'") unless $evolverexe && -e $evolverexe && -x _; open(RUN, "$evolverexe 6 MCcodon.dat |") or $self->throw("Cannot open exe $evolverexe"); my @output = ; $exit_status = close(RUN); $self->error_string(join('',@output)); if ( (grep { /\berr(or)?: /io } @output) || !$exit_status) { $self->warn("There was an error - see error_string for the program output"); $rc = 0; } # FIXME - hardcoded mc.paml unless ($self->indel) { my $in = Bio::AlignIO->new('-file' => "$tmpdir/mc.paml", '-format' => 'phylip'); my $aln = $in->next_aln(); $self->alignment($aln); } } return $rc; } sub error_string{ my ($self,$value) = @_; if( defined $value) { $self->{'error_string'} = $value; } return $self->{'error_string'}; } sub alignment{ my ($self,$aln) = @_; if( defined $aln ) { if( -e $aln ) { $self->{'_alignment'} = $aln; } elsif( !ref($aln) || ! $aln->isa('Bio::Align::AlignI') ) { $self->warn("Must specify a valid Bio::Align::AlignI object to the alignment function not $aln"); return undef; } else { $self->{'_alignment'} = $aln; } } return $self->{'_alignment'}; } sub tree { my ($self, $tree, %params) = @_; if( defined $tree ) { if( ! ref($tree) || ! $tree->isa('Bio::Tree::TreeI') ) { $self->warn("Must specify a valid Bio::Tree::TreeI object to the alignment function"); } $self->{'_tree'} = $tree; # FIXME: I think we dont need this in Evolver # if ( defined $params{'_branchLengths'} ) { # my $ubl = $params{'_branchLengths'}; # if ($ubl !~ m/^(0|1|2)$/) { # $self->throw("The branchLengths parameter to tree() must be 0 (ignore), 1 (initial values) or 2 (fixed values) only"); # } # $self->{'_branchLengths'} = $ubl; # } } return $self->{'_tree'}; } sub get_parameters{ my ($self) = @_; # we're returning a copy of this return %{ $self->{'_evolverparams'} }; } sub set_parameter{ my ($self,$param,$value) = @_; unless ($self->{'no_param_checks'} == 1) { if ( ! defined $VALIDVALUES{$param} ) { $self->warn("unknown parameter $param will not be set unless you force by setting no_param_checks to true"); return 0; } if ( ref( $VALIDVALUES{$param}) =~ /ARRAY/i && scalar @{$VALIDVALUES{$param}} > 0 ) { unless ( grep { $value eq $_ } @{ $VALIDVALUES{$param} } ) { $self->warn("parameter $param specified value $value is not recognized, please see the documentation and the code for this module or set the no_param_checks to a true value"); return 0; } } } $self->{'_evolverparams'}->{$param} = $value; return 1; } sub set_default_parameters{ my ($self,$keepold) = @_; $keepold = 0 unless defined $keepold; while( my ($param,$val) = each %VALIDVALUES ) { # skip if we want to keep old values and it is already set next if( defined $self->{'_evolverparams'}->{$param} && $keepold); if(ref($val)=~/ARRAY/i ) { $self->{'_evolverparams'}->{$param} = $val->[0]; } else { $self->{'_evolverparams'}->{$param} = $val; } } } sub no_param_checks{ my ($self,$value) = @_; if( defined $value) { $self->{'no_param_checks'} = $value; } return $self->{'no_param_checks'}; } sub set_CodonFreqs{ my $self = shift; return $self->{'_codonfreqs'} = shift if @_; return $self->{'_codonfreqs'}; } sub get_CodonFreqs{ my ($self) = @_; return @{$self->{'_codonfreqs'} || []}; } sub DESTROY { my $self= shift; unless ( $self->save_tempfiles ) { $self->cleanup(); } $self->SUPER::DESTROY(); } sub indel{ my $self = shift; return $self->{'indel'} = shift if @_; return $self->{'indel'}; } 1; __END__ =pod =encoding UTF-8 =head1 NAME Bio::Tools::Run::Phylo::PAML::Evolver - Wrapper aroud the PAML program evolver =head1 VERSION version 1.7.3 =head1 SYNOPSIS use Bio::Tools::Run::Phylo::PAML::Evolver; my $evolver = Bio::Tools::Run::Phylo::PAML::Evolver->new(); # Get a $tree object somehow $evolver->tree($tree); # FIXME: evolver generates a tree (first run with option 1 or 2)? # One or more alns are created my @alns = $evolver->run(); #### # Or with all the data coming from a previous PAML run my $parser = Bio::Tools::Phylo::PAML->new ( -file => "$inputfile", ); my $result = $parser->next_result(); my $tree = $result->next_tree; $evolver->tree($tree); my @codon_freqs = $result->get_CodonFreqs(); $evolver->set_CodonFreqs(\@codon_freqs); my $val = $evolver->prepare(); # FIXME: something similar for nucleotide frequencies: # Option (5) Simulate nucleotide data sets (use MCbase.dat)? # FIXME: something similar for aa parameters: # Option (7) Simulate amino acid data sets (use MCaa.dat)? # FIXME: With an initial RootSeq.txt =head1 DESCRIPTION This is a wrapper around the evolver program of PAML (Phylogenetic Analysis by Maximum Likelihood) package of Ziheng Yang. See http://abacus.gene.ucl.ac.uk/software/paml.html for more information. This module is more about generating the properl MCmodel.ctl file and will run the program in a separate temporary directory to avoid creating temp files all over the place. =head2 Default Values Valid and default values for evolver programs are listed below. The default values are always the first one listed. These descriptions are essentially lifted from the example MCcodon.dat file and pamlDOC documentation provided by the author. Stub: B specifies something. B specifies something else. INCOMPLETE DOCUMENTATION OF ALL METHODS =head1 ATTRIBUTES =head2 program_name Title : program_name Usage : $factory->program_name() Function: holds the program name Returns: string Args : None =head2 program_dir Title : program_dir Usage : ->program_dir() Function: returns the program directory, obtained from ENV variable. Returns: string Args : =head2 error_string Title : error_string Usage : $obj->error_string($newval) Function: Where the output from the last analysis run is stored. Returns : value of error_string Args : newvalue (optional) =head2 alignment Title : alignment Usage : $evolver->align($aln); Function: Get/Set the L object Returns : L object Args : [optional] L Comment : We could potentially add support for running directly on a file but we shall keep it simple See also: L =head2 tree Title : tree Usage : $evolver->tree($tree, %params); Function: Get/Set the L object Returns : L Args : [optional] $tree => L, [optional] %parameters => hash of tree-specific parameters: branchLengths: 0, 1 or 2 out Comment : We could potentially add support for running directly on a file but we shall keep it simple See also: L =head2 no_param_checks Title : no_param_checks Usage : $obj->no_param_checks($newval) Function: Boolean flag as to whether or not we should trust the sanity checks for parameter values Returns : value of no_param_checks Args : newvalue (optional) =head2 save_tempfiles Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional) =head2 outfile_name Title : outfile_name Usage : my $outfile = $evolver->outfile_name(); Function: Get/Set the name of the output file for this run (if you wanted to do something special) Returns : string Args : [optional] string to set value to =head2 tempdir Title : tempdir Usage : my $tmpdir = $self->tempdir(); Function: Retrieve a temporary directory name (which is created) Returns : string which is the name of the temporary directory Args : none =head2 indel Title : indel Usage : $obj->indel($newval) Function: this is only useful if using evolver_indel instead of main evolver package: Exploring the Relationship between Sequence Similarity and Accurate Phylogenetic Trees Brandi L. Cantarel, Hilary G. Morrison and William Pearson Example : Returns : value of indel (a scalar) Args : on set, new value (a scalar or undef, optional) =head1 METHODS =head2 new Title : new Usage : my $obj = Bio::Tools::Run::Phylo::PAML::Evolver->new(); Function: Builds a new Bio::Tools::Run::Phylo::PAML::Evolver object Returns : Bio::Tools::Run::Phylo::PAML::Evolver -save_tempfiles => boolean to save the generated tempfiles and NOT cleanup after onesself (default FALSE) -tree => the Bio::Tree::TreeI object (FIXME: optional if this is done in a first run) -params => a hashref of PAML parameters (all passed to set_parameter) -executable => where the evolver executable resides See also: L =head2 prepare Title : prepare Usage : my $rundir = $evolver->prepare($aln); Function: prepare the evolver analysis using the default or updated parameters the alignment parameter must have been set Returns : value of rundir Args : L object, L object [optional] =head2 run Title : run Usage : my ($rc,$parser) = $evolver->run(); Function: run the evolver analysis using the default or updated parameters the alignment parameter must have been set Returns : Return code, L Args : L object, L object [optional] =head2 get_parameters Title : get_parameters Usage : my %params = $self->get_parameters(); Function: returns the list of parameters as a hash Returns : associative array keyed on parameter names Args : none =head2 set_parameter Title : set_parameter Usage : $evolver->set_parameter($param,$val); Function: Sets a evolver parameter, will be validated against the valid values as set in the %VALIDVALUES class variable. The checks can be ignored if one turns off param checks like this: $evolver->no_param_checks(1) Returns : boolean if set was success, if verbose is set to -1 then no warning will be reported Args : $param => name of the parameter $value => value to set the parameter to See also: L =head2 set_default_parameters Title : set_default_parameters Usage : $evolver->set_default_parameters(0); Function: (Re)set the default parameters from the defaults (the first value in each array in the %VALIDVALUES class variable) Returns : none Args : boolean: keep existing parameter values =head2 set_CodonFreqs Title : set_CodonFreqs Usage : $obj->set_CodonFreqs($newval) Function: Get/Set the Codon Frequence table Returns : value of set_CodonFreqs (a scalar) Args : on set, new value (a scalar or undef, optional) =head2 get_CodonFreqs Title : get_CodonFreqs Usage : my @codon_freqs = $evolver->get_CodonFreqs() Function: Get the Codon freqs Returns : Array Args : none =head2 cleanup Title : cleanup Usage : $evolver->cleanup(); Function: Will cleanup the tempdir directory after a PAML run Returns : none Args : none =head2 io Title : io Usage : $obj->io($newval) Function: Gets a L object Returns : L Args : none =head1 Bio::Tools::Run::WrapperBase methods =head1 FEEDBACK =head2 Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bio-tools-phylo-paml/issues =head1 AUTHOR Albert Vilella =head1 COPYRIGHT This software is copyright (c) by Albert Vilella . This software is available under the same terms as the perl 5 programming language system itself. =cut Bio-Tools-Phylo-PAML-1.7.3/lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm0000644000175000017500000003206013316145226024210 0ustar carandraugcarandraugpackage Bio::Tools::Run::Phylo::PAML::Yn00; $Bio::Tools::Run::Phylo::PAML::Yn00::VERSION = '1.7.3'; use utf8; use strict; use warnings; use vars qw(@ISA %VALIDVALUES $MINNAMELEN $PROGRAMNAME $PROGRAM); use Cwd; use Bio::Root::Root; use Bio::AlignIO; use Bio::TreeIO; use Bio::Tools::Run::WrapperBase; use Bio::Tools::Phylo::PAML; @ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase); # ABSTRACT: Wrapper aroud the PAML program yn00 # AUTHOR: Jason Stajich # OWNER: Jason Stajich # LICENSE: Perl_5 BEGIN { $MINNAMELEN = 25; $PROGRAMNAME = 'yn00' . ($^O =~ /mswin/i ?'.exe':''); if( defined $ENV{'PAMLDIR'} ) { $PROGRAM = Bio::Root::IO->catfile($ENV{'PAMLDIR'},$PROGRAMNAME); } # valid values for parameters, the default one is always # the first one in the array # much of the documentation here is lifted directly from the codeml.ctl # example file provided with the package %VALIDVALUES = ( 'noisy' => [ 0..3,9], 'verbose' => [ 0,1,2], # 0:concise, 1:detailed, 2:too much 'weighting' => [0,1], # weighting pathways between codons 'commonf3x4' => [0,1], # use same f3x4 for all sites # (icode) genetic code # 0:universal code # 1:mamalian mt # 2:yeast mt # 3:mold mt, # 4:invertebrate mt # 5:ciliate nuclear # 6:echinoderm mt # 7:euplotid mt # 8:alternative yeast nu. # 9:ascidian mt #10:blepharisma nu # these correspond to 1-11 in the genbank transl table 'icode' => [ 0..10], 'ndata' => [1..10], ); } sub program_name { return $PROGRAMNAME; } sub program_dir { return Bio::Root::IO->catfile($ENV{PAMLDIR}) if $ENV{PAMLDIR}; } sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($aln,$st) = $self->_rearrange([qw(ALIGNMENT SAVE_TEMPFILES)], @args); defined $aln && $self->alignment($aln); defined $st && $self->save_tempfiles($st); $self->set_default_parameters(); return $self; } sub run{ my ($self,$aln) = @_; ($aln) ||= $self->alignment(); if( ! $aln ) { $self->warn("must have supplied a valid alignment file in order to run yn00"); return 0; } my ($tmpdir) = $self->tempdir(); my ($tempseqFH,$tempseqfile); if( ! ref($aln) && -e $aln ) { $tempseqfile = $aln; } else { ($tempseqFH,$tempseqfile) = $self->io->tempfile ('-dir' => $tmpdir, UNLINK => ($self->save_tempfiles ? 0 : 1)); my $alnout = Bio::AlignIO->new('-format' => 'phylip', '-fh' => $tempseqFH, '-interleaved' => 0, '-idlength' => $MINNAMELEN > $aln->maxdisplayname_length() ? $MINNAMELEN : $aln->maxdisplayname_length() +1); $alnout->write_aln($aln); $alnout->close(); undef $alnout; close($tempseqFH); undef $tempseqFH; } # now let's print the yn.ctl file. # many of the these programs are finicky about what the filename is # and won't even run without the properly named file. Ack my $yn_ctl = "$tmpdir/yn00.ctl"; open(YN, ">$yn_ctl") or $self->throw("cannot open $yn_ctl for writing"); print YN "seqfile = $tempseqfile\n"; my $outfile = $self->outfile_name; print YN "outfile = $outfile\n"; my %params = $self->get_parameters; while( my ($param,$val) = each %params ) { print YN "$param = $val\n"; } close(YN); my ($rc,$parser) = (1); { my $cwd = cwd(); my $exit_status; chdir($tmpdir); my $ynexe = $self->executable(); $self->throw("unable to find executable for 'yn'") unless $ynexe; open(RUN, "$ynexe |"); my @output = ; $exit_status = close(RUN); $self->error_string(join('',@output)); if( (grep { /\berr(or)?: /io } @output) || !$exit_status ) { $self->warn("There was an error - see error_string for the program output"); $rc = 0; } eval { $parser = Bio::Tools::Phylo::PAML->new(-file => "$tmpdir/mlc", -dir => "$tmpdir"); }; if( $@ ) { $self->warn($self->error_string); } chdir($cwd); } if( $self->verbose > 0 ) { open(IN, "$tmpdir/mlc"); while() { $self->debug($_); } } unless ( $self->save_tempfiles ) { unlink("$yn_ctl"); $self->cleanup(); } return ($rc,$parser); } sub error_string{ my ($self,$value) = @_; if( defined $value) { $self->{'error_string'} = $value; } return $self->{'error_string'}; } sub alignment{ my ($self,$aln) = @_; if( defined $aln ) { if( !ref($aln) || ! $aln->isa('Bio::Align::AlignI') ) { $self->warn("Must specify a valid Bio::Align::AlignI object to the alignment function"); return undef; } $self->{'_alignment'} = $aln; } return $self->{'_alignment'}; } sub get_parameters{ my ($self) = @_; # we're returning a copy of this return %{ $self->{'_codemlparams'} }; } sub set_parameter{ my ($self,$param,$value) = @_; if( ! defined $VALIDVALUES{$param} ) { $self->warn("unknown parameter $param will not set unless you force by setting no_param_checks to true"); return 0; } if( ref( $VALIDVALUES{$param}) =~ /ARRAY/i && scalar @{$VALIDVALUES{$param}} > 0 ) { unless ( grep {$value} @{ $VALIDVALUES{$param} } ) { $self->warn("parameter $param specified value $value is not recognized, please see the documentation and the code for this module or set the no_param_checks to a true value"); return 0; } } $self->{'_codemlparams'}->{$param} = $value; return 1; } sub set_default_parameters{ my ($self,$keepold) = @_; $keepold = 0 unless defined $keepold; while( my ($param,$val) = each %VALIDVALUES ) { # skip if we want to keep old values and it is already set next if( defined $self->{'_codemlparams'}->{$param} && $keepold); if(ref($val)=~/ARRAY/i ) { $self->{'_codemlparams'}->{$param} = $val->[0]; } else { $self->{'_codemlparams'}->{$param} = $val; } } } 1; __END__ =pod =encoding UTF-8 =head1 NAME Bio::Tools::Run::Phylo::PAML::Yn00 - Wrapper aroud the PAML program yn00 =head1 VERSION version 1.7.3 =head1 SYNOPSIS use Bio::Tools::Run::Phylo::PAML::Yn00; use Bio::AlignIO; my $alignio = Bio::AlignIO->new(-format => 'phylip', -file => 't/data/gf-s85.phylip'); my $aln = $alignio->next_aln; my $yn = Bio::Tools::Run::Phylo::PAML::Yn00->new(); $yn->alignment($aln); my ($rc,$parser) = $yn->run(); while( my $result = $parser->next_result ) { my @otus = $result->get_seqs(); my $MLmatrix = $result->get_MLmatrix(); # 0 and 1 correspond to the 1st and 2nd entry in the @otus array my $dN = $MLmatrix->[0]->[1]->{dN}; my $dS = $MLmatrix->[0]->[1]->{dS}; my $kaks =$MLmatrix->[0]->[1]->{omega}; print "Ka = $dN Ks = $dS Ka/Ks = $kaks\n"; } =head1 DESCRIPTION This is a wrapper around the yn00 (method of Yang and Nielsen, 2000) program of PAML (Phylogenetic Analysis by Maximum Likelihood) package of Ziheng Yang. See http://abacus.gene.ucl.ac.uk/software/paml.html for more information. This module will generate a proper yn00.ctl file and will run the program in a separate temporary directory to avoid creating temp files all over the place and will cleanup after itself. =head2 Default Values See the L module for documentation of the default values. =head1 ATTRIBUTES =head2 program_name Title : program_name Usage : $yn00->program_name() Function: holds the program name Returns: string Args : None =head2 program_dir Title : program_dir Usage : $yn00->program_dir() Function: returns the program directory, obtained from ENV variable. Returns: string Args : =head2 error_string Title : error_string Usage : $obj->error_string($newval) Function: Where the output from the last analysus run is stored. Returns : value of error_string Args : newvalue (optional) =head2 alignment Title : alignment Usage : $codeml->align($aln); Function: Get/Set the L object Returns : L object Args : [optional] L Comment : We could potentially add support for running directly on a file but we shall keep it simple See also: L =head2 no_param_checks Title : no_param_checks Usage : $obj->no_param_checks($newval) Function: Boolean flag as to whether or not we should trust the sanity checks for parameter values Returns : value of no_param_checks Args : newvalue (optional) =head2 save_tempfiles Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional) =head2 outfile_name Title : outfile_name Usage : my $outfile = $codeml->outfile_name(); Function: Get/Set the name of the output file for this run (if you wanted to do something special) Returns : string Args : [optional] string to set value to =head2 tempdir Title : tempdir Usage : my $tmpdir = $self->tempdir(); Function: Retrieve a temporary directory name (which is created) Returns : string which is the name of the temporary directory Args : none =head1 METHODS =head2 new Title : new Usage : my $obj = Bio::Tools::Run::Phylo::PAML::Yn00->new(); Function: Builds a new Bio::Tools::Run::Phylo::PAML::Yn00 object Returns : Bio::Tools::Run::Phylo::PAML::Yn00 Args : -alignment => the L object -save_tempfiles => boolean to save the generated tempfiles and NOT cleanup after onesself (default FALSE) =head2 run Title : run Usage : $yn->run(); Function: run the yn00 analysis using the default or updated parameters the alignment parameter must have been set Returns : 3 values, $rc = 1 for success, 0 for errors hash reference of the Yang calculated Ka/Ks values this is a set of pairwise observations keyed as sequencenameA->sequencenameB->datatype hash reference same as the previous one except it for the Nei and Gojobori calculated Ka,Ks,omega values Args : none =head2 get_parameters Title : get_parameters Usage : my %params = $self->get_parameters(); Function: returns the list of parameters as a hash Returns : associative array keyed on parameter names Args : none =head2 set_parameter Title : set_parameter Usage : $codeml->set_parameter($param,$val); Function: Sets a codeml parameter, will be validated against the valid values as set in the %VALIDVALUES class variable. The checks can be ignored if on turns of param checks like this: $codeml->no_param_checks(1) Returns : boolean if set was success, if verbose is set to -1 then no warning will be reported Args : $paramname => name of the parameter $value => value to set the parameter to See also: L =head2 set_default_parameters Title : set_default_parameters Usage : $codeml->set_default_parameters(0); Function: (Re)set the default parameters from the defaults (the first value in each array in the %VALIDVALUES class variable) Returns : none Args : boolean: keep existing parameter values =head2 cleanup Title : cleanup Usage : $codeml->cleanup(); Function: Will cleanup the tempdir directory after a PAML run Returns : none Args : none =head2 io Title : io Usage : $obj->io($newval) Function: Gets a L object Returns : L Args : none =head1 Bio::Tools::Run::Wrapper methods =head1 FEEDBACK =head2 Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bio-tools-phylo-paml/issues =head1 AUTHOR Jason Stajich =head1 COPYRIGHT This software is copyright (c) by Jason Stajich . This software is available under the same terms as the perl 5 programming language system itself. =cut Bio-Tools-Phylo-PAML-1.7.3/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm0000644000175000017500000004777613316145226024711 0ustar carandraugcarandraugpackage Bio::Tools::Run::Phylo::PAML::Baseml; $Bio::Tools::Run::Phylo::PAML::Baseml::VERSION = '1.7.3'; use utf8; use strict; use warnings; use vars qw(@ISA %VALIDVALUES $MINNAMELEN $PROGRAMNAME $PROGRAM); use Cwd; use Bio::AlignIO; use Bio::TreeIO; use Bio::Tools::Phylo::PAML; use base qw(Bio::Tools::Run::Phylo::PhyloBase); # ABSTRACT: Wrapper aroud the PAML program baseml # AUTHOR: Jason Stajich # OWNER: Jason Stajich # LICENSE: Perl_5 # AUTHOR: Sendu Bala BEGIN { $MINNAMELEN = 25; $PROGRAMNAME = 'baseml' . ($^O =~ /mswin/i ?'.exe':''); if( defined $ENV{'PAMLDIR'} ) { $PROGRAM = Bio::Root::IO->catfile($ENV{'PAMLDIR'},$PROGRAMNAME); } # valid values for parameters, the default one is always # the first one in the array # much of the documentation here is lifted directly from the baseml.ctl # example file provided with the package %VALIDVALUES = ( 'noisy' => [ 0..3,9], 'verbose' => [ 0,1,2], # 0:concise, 1:detailed, 2:too much 'runmode' => [0..5], # for runmode # 0: use the provided tree structure(s) in treefile # 1,2: mean heuristic search by star-decomposition alg # 2: starts from star tree while 1 reads a multifurcating # tree from treefile and ties to estimate the best # bifurcating tree # 3: stepwise addition # 4: NNI perturbation with the starting tree # Tree search DOES NOT WORK WELL so estimate a tree # using other programs first 'model' => [5, 0..8], # for model # 0: JC69 (uncorrected) # 1: K80 (transitions/transversion weighted differently) # 2: F81 # 3: F84 # 4: HKY85 # 5: T92 (Tamura 92) # 6: TN93 (Tajima-Nei) correct for multiple substitutions # 7: REV (aka GTR) # 8: UNREST # See Yang 1994 JME 39:105-111 # model 8 special case of the REV model # model 9 is special case of unrestricted model # can also supply special rate parameters # so for example (from pamlDOC.pdf # $model = '8 [2 (CT) (AG)]'; # TN93 # $model = '8 [2 (TA AT TG CA CG) (AG)]'; # TN93 # $model = '9 [1 (TC CT AG GA)]; # K80 # $model = '9 [0]'; # JC69 # $model = '9 [11 (TA) (TG) (CT) (CA) (CG) (AT) (AC) (AG) (GT) (GC) (GA)], 'outfile' => 'mlb', 'fix_kappa'=> [0,1], # 0:estimate kappa, 1:fix kappa 'kappa' => '2.5', # initial or fixed kappa 'fix_alpha'=> [1,0], # 0: estimate gamma shape param # 1: fix it at alpha 'alpha' => '0', # initial of fixed alpha # 0: infinity (constant rate) 'Malpha' => [0,1], # different alphas for genes 'fix_rho'=> [1,0], # 0: estimate gamma shape param # 1: fix it at alpha 'rho' => '0', # initial of fixed alpha # 0: infinity (constant rate) 'ncatG' => '5', # number of categories in the dD,AdG, or nparkK models of rates 'nparK' => [0..4], # rate-class models # 1:rk 2:rk&fK # 3:rK&MK(1/K) 4:rK&MK 'nhomo' => [0..4], # 0 & 1: homogeneous, # 2: kappa for brances # 3:N1 4:N2 'getSE' => [0,1], 'RateAncestor' => [0,1,2], # rates (alpha > 0) or # ancestral states 'cleandata' => [1,0], # remove sites with # ambiguity data (1:yes or 0:no) 'fix_blength' => [0,-1,1,2], # 0: ignore, -1: random, # 1: initial, 2: fixed 'icode' => [ 0..10], # (with RateAncestor=1. #try "GC" in data,model=4,Mgene=4) 'ndata' => [1..10], 'clock' => [0..3], # 0: no clock, 1: clock, 2: local clock, 3: CombinedAnalysis 'Small_Diff' => '1e-6', #underflow issues? 'Mgene' => [0..4], # 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff ); } sub program_name { return $PROGRAMNAME; } sub program_dir { return Bio::Root::IO->catfile($ENV{PAMLDIR}) if $ENV{PAMLDIR}; } sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($aln,$tree,$st) = $self->_rearrange([qw(ALIGNMENT TREE SAVE_TEMPFILES)], @args); defined $aln && $self->alignment($aln); defined $tree && $self->tree($tree); defined $st && $self->save_tempfiles($st); return $self; } sub run { my ($self, $aln, $tree) = @_; $aln = $self->alignment($aln) if $aln; $tree = $self->tree($tree) if $tree; $aln ||= $self->alignment(); $tree ||= $self->tree(); my %params = $self->get_parameters; if( ! $aln ) { $self->warn("must have supplied a valid aligment file in order to run baseml"); return 0; } if ((defined $params{runmode} && ($params{runmode} == 0 || $params{runmode} == 1)) && ! $tree) { $self->warn("must have supplied a tree in order to run baseml in runmode 0 or 1"); return 0; } # replace spaces with underscores in ids, since baseml really doesn't like # spaces (actually, the resulting double quotes) in tree ids if ($tree) { my $changed = 0; foreach my $thing ($aln->each_seq, $tree ? $tree->get_leaf_nodes : ()) { my $id = $thing->id; if ($id =~ / /) { $id =~ s/\s+/_/g; $thing->id($id); $changed = 1; } } if ($changed) { my $new_aln = $aln->new; foreach my $seq ($aln->each_seq) { $new_aln->add_seq($seq); } $aln = $new_aln; $aln = $self->alignment($aln); $tree = $self->tree($tree); } # check node and seq names match $self->_check_names; } # output the alignment and tree to tempfiles my $tempseqfile = $self->_write_alignment('phylip', -interleaved => 0, -idlinebreak => 1, -line_length => 60, -wrap_sequential => 1, -idlength => $MINNAMELEN > $aln->maxdisplayname_length() ? $MINNAMELEN : $aln->maxdisplayname_length() +1); $tree = $self->_write_tree() if $tree; # now let's print the baseml.ctl file. # many of the these programs are finicky about what the filename is # and won't even run without the properly named file. Ack my $tmpdir = $self->tempdir(); my $baseml_ctl = "$tmpdir/baseml.ctl"; open(my $mlfh, ">$baseml_ctl") or $self->throw("cannot open $baseml_ctl for writing"); print $mlfh "seqfile = $tempseqfile\n"; print $mlfh "treefile = $tree\n" if $tree; my $outfile = $self->outfile_name; print $mlfh "outfile = $outfile\n"; while( my ($param,$val) = each %params ) { next if $param eq 'outfile'; print $mlfh "$param = $val\n"; } close($mlfh); my ($rc,$parser) = (1); { my $cwd = cwd(); my $exit_status; chdir($tmpdir); my $ynexe = $self->executable(); $self->throw("unable to find executable for 'baseml'") unless $ynexe; open(my $run, "$ynexe |"); my @output = <$run>; $exit_status = close($run); $self->error_string(join('', grep { /\berr(or)?: /io } @output)); if ($self->error_string || !$exit_status) { $self->warn("There was an error - see error_string for the program output"); $rc = 0; } eval { $parser = Bio::Tools::Phylo::PAML->new(-file => "$tmpdir/mlb", -dir => "$tmpdir"); }; if( $@ ) { $self->warn($self->error_string); } chdir($cwd); } if( $self->verbose > 0 ) { open(my $in, "$tmpdir/mlb"); while(<$in>) { $self->debug($_); } close($in); } return ($rc,$parser); } sub error_string { my ($self,$value) = @_; if( defined $value) { chomp($value); $self->{'error_string'} = $value; } return $self->{'error_string'}; } sub alignment{ my $self = shift; return $self->_alignment(@_); } sub tree { my $self = shift; return $self->_tree(@_); } sub get_parameters{ my ($self) = @_; # we're returning a copy of this return %{ $self->{'_basemlparams'} }; } sub set_parameter{ my ($self,$param,$value) = @_; if( ! defined $VALIDVALUES{$param} ) { $self->warn("unknown parameter $param will not set unless you force by setting no_param_checks to true"); return 0; } if( ref( $VALIDVALUES{$param}) =~ /ARRAY/i && scalar @{$VALIDVALUES{$param}} > 0 ) { my %allowed = map { $_ => 1 } @{ $VALIDVALUES{$param} }; unless ( exists $allowed{$value} ) { $self->warn("parameter $param specified value $value is not recognized, please see the documentation and the code for this module or set the no_param_checks to a true value"); return 0; } } $self->{'_basemlparams'}->{$param} = $value; return 1; } sub set_default_parameters{ my ($self,$keepold) = @_; $keepold = 0 unless defined $keepold; while( my ($param,$val) = each %VALIDVALUES ) { # skip if we want to keep old values and it is already set next if( defined $self->{'_basemlparams'}->{$param} && $keepold); if(ref($val)=~/ARRAY/i ) { $self->{'_basemlparams'}->{$param} = $val->[0]; } else { $self->{'_basemlparams'}->{$param} = $val; } } } sub outfile_name { my $self = shift; if( @_ ) { return $self->{'_basemlparams'}->{'outfile'} = shift @_; } unless (defined $self->{'_basemlparams'}->{'outfile'}) { $self->{'_basemlparams'}->{'outfile'} = 'mlb'; } return $self->{'_basemlparams'}->{'outfile'}; } 1; __END__ =pod =encoding UTF-8 =head1 NAME Bio::Tools::Run::Phylo::PAML::Baseml - Wrapper aroud the PAML program baseml =head1 VERSION version 1.7.3 =head1 SYNOPSIS use Bio::Tools::Run::Phylo::PAML::Baseml; use Bio::AlignIO; my $alignio = Bio::AlignIO->new(-format => 'phylip', -file => 't/data/gf-s85.phylip'); my $aln = $alignio->next_aln; my $bml = Bio::Tools::Run::Phylo::PAML::Baseml->new(); $bml->alignment($aln); my ($rc,$parser) = $bml->run(); while( my $result = $parser->next_result ) { my @otus = $result->get_seqs(); my $MLmatrix = $result->get_MLmatrix(); # 0 and 1 correspond to the 1st and 2nd entry in the @otus array } =head1 DESCRIPTION This is a wrapper around the baseml program of PAML (Phylogenetic Analysis by Maximum Likelihood) package of Ziheng Yang. See http://abacus.gene.ucl.ac.uk/software/paml.html for more information. This module will generate a proper baseml.ctl file and will run the program in a separate temporary directory to avoid creating temp files all over the place and will cleanup after itself.. The values you can feed to the configuration file are documented here. 'noisy' => [ 0..3,9], 'verbose' => [ 0,1,2], # 0:concise, 1:detailed, 2:too much 'runmode' => [0..5], # for runmode # 0: use the provided tree structure(s) in treefile # 1,2: mean heuristic search by star-decomposition alg # 2: starts from star tree while 1 reads a multifurcating # tree from treefile and ties to estimate the best # bifurcating tree # 3: stepwise addition # 4: NNI perturbation with the starting tree # Tree search DOES NOT WORK WELL so estimate a tree # using other programs first 'model' => '0', # for model # 0: JC69 (uncorrected) # 1: K80 (transitions/transversion weighted differently) # 2: F81 # 3: F84 # 4: HKY85 # 5: T92 (Tamura 92) # 6: TN93 (Tajima-Nei) correct for multiple substitutions # 7: REV (aka GTR) # 8: UNREST # 9: REVu #10: UNRESTu # See Yang 1994 JME 39:105-111 # model 8 special case of the REV model # model 9 is special case of unrestricted model # can also supply special rate parameters # so for example (from pamlDOC.pdf # $model = '8 [2 (CT) (AG)]'; # TN93 # $model = '8 [2 (TA AT TG CA CG) (AG)]'; # TN93 # $model = '9 [1 (TC CT AG GA)]; # K80 # $model = '9 [0]'; # JC69 # $model = '9 [11 (TA) (TG) (CT) (CA) (CG) (AT) (AC) (AG) (GT) (GC) (GA)], 'outfile' => 'mlb', 'fix_kappa'=> [0,1], # 0:estimate kappa, 1:fix kappa 'kappa' => '2.5', # initial or fixed kappa 'fix_alpha'=> [1,0], # 0: estimate gamma shape param # 1: fix it at alpha 'alpha' => '0', # initial of fixed alpha # 0: infinity (constant rate) 'Malpha' => [0,1], # different alphas for genes 'fix_rho'=> [1,0], # 0: estimate gamma shape param # 1: fix it at alpha 'rho' => '0', # initial of fixed alpha # 0: infinity (constant rate) 'ncatG' => '5', # number of categories in the dD,AdG, or nparkK models of rates 'nparK' => [0..4], # rate-class models # 1:rk 2:rk&fK # 3:rK&MK(1/K) 4:rK&MK 'nhomo' => [0..4], # 0 & 1: homogeneous, # 2: kappa for brances # 3:N1 4:N2 'getSE' => [0,1], 'RateAncestor' => [1,0,2], # rates (alpha > 0) or # ancestral states 'cleandata' => [1,0], # remove sites with # ambiguity data (1:yes or 0:no) 'fix_blength' => [-1,0,1,2], # 0: ignore, -1: random, # 1: initial, 2: fixed # 'icode' => [ 0..10], # (with RateAncestor=1. #try "GC" in data,model=4,Mgene=4) 'ndata' => [5,1..10], 'clock' => [0..3], # 0: no clock, 1: clock, 2: local clock, 3: CombinedAnalysis 'Small_Diff' => '1e-6', #underflow issues? =head1 ATTRIBUTES =head2 program_name Title : program_name Usage : $obj->program_name() Function: holds the program name Returns: string Args : None =head2 program_dir Title : program_dir Usage : ->program_dir() Function: returns the program directory, obtained from ENV variable. Returns: string Args : =head2 error_string Title : error_string Usage : $obj->error_string($newval) Function: Where the output from the last analysus run is stored. Returns : value of error_string Args : newvalue (optional) =head2 alignment Title : alignment Usage : $baseml->alignment($aln); Function: Get/Set the L object Returns : L object Args : [optional] L Comment : We could potentially add support for running directly on a file but we shall keep it simple See also: L =head2 tree =head2 no_param_checks Title : no_param_checks Usage : $obj->no_param_checks($newval) Function: Boolean flag as to whether or not we should trust the sanity checks for parameter values Returns : value of no_param_checks Args : newvalue (optional) =head2 save_tempfiles Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional) =head2 outfile_name Title : outfile_name Usage : my $outfile = $baseml->outfile_name(); Function: Get/Set the name of the output file for this run (if you wanted to do something special) Returns : string Args : [optional] string to set value to =head2 tempdir Title : tempdir Usage : my $tmpdir = $self->tempdir(); Function: Retrieve a temporary directory name (which is created) Returns : string which is the name of the temporary directory Args : none =head1 METHODS =head2 new Title : new Usage : my $obj = Bio::Tools::Run::Phylo::PAML::Baseml->new(); Function: Builds a new Bio::Tools::Run::Phylo::PAML::Baseml object Returns : Bio::Tools::Run::Phylo::PAML::Baseml Args : -alignment => the L object -tree => the L object if you want to use runmode 0 or 1 -save_tempfiles => boolean to save the generated tempfiles and NOT cleanup after onesself (default FALSE) =head2 run Title : run Usage : $yn->run(); Function: run the Baseml analysis using the default or updated parameters the alignment parameter must have been set Returns : 3 values, $rc = 1 for success, 0 for errors hash reference of the Yang calculated Ka/Ks values this is a set of pairwise observations keyed as sequencenameA->sequencenameB->datatype hash reference same as the previous one except it for the Nei and Gojobori calculated Ka,Ks,omega values Args : optionally, a value appropriate for alignment() and one for tree() NB : Since Baseml doesn't handle spaces in tree node ids, if a tree is in use spaces will be converted to underscores in both the tree node ids and alignment sequence ids. =head2 get_parameters Title : get_parameters Usage : my %params = $self->get_parameters(); Function: returns the list of parameters as a hash Returns : associative array keyed on parameter names Args : none =head2 set_parameter Title : set_parameter Usage : $baseml->set_parameter($param,$val); Function: Sets a baseml parameter, will be validated against the valid values as set in the %VALIDVALUES class variable. The checks can be ignored if on turns of param checks like this: $baseml->no_param_checks(1) Returns : boolean if set was success, if verbose is set to -1 then no warning will be reported Args : $paramname => name of the parameter $value => value to set the parameter to See also: L =head2 set_default_parameters Title : set_default_parameters Usage : $baseml->set_default_parameters(0); Function: (Re)set the default parameters from the defaults (the first value in each array in the %VALIDVALUES class variable) Returns : none Args : boolean: keep existing parameter values NB : using this isn't an especially good idea! You don't need to do anything to end up using default parameters: hence 'default'! =head2 cleanup Title : cleanup Usage : $baseml->cleanup(); Function: Will cleanup the tempdir directory after a PAML run Returns : none Args : none =head2 io Title : io Usage : $obj->io($newval) Function: Gets a L object Returns : L Args : none =head1 Bio::Tools::Run::Wrapper methods =head1 FEEDBACK =head2 Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bio-tools-phylo-paml/issues =head1 AUTHORS Jason Stajich Sendu Bala =head1 COPYRIGHT This software is copyright (c) by Jason Stajich . This software is available under the same terms as the perl 5 programming language system itself. =cut Bio-Tools-Phylo-PAML-1.7.3/Makefile.PL0000644000175000017500000000531013316145226020125 0ustar carandraugcarandraug# This file was automatically generated by Dist::Zilla::Plugin::MakeMaker v6.012. use strict; use warnings; # inserted by Dist::Zilla::Plugin::CheckBin 0.008 use Devel::CheckBin; check_bin('basemlg'); check_bin('codeml'); check_bin('evolver'); check_bin('yn00'); use 5.006; use ExtUtils::MakeMaker; my %WriteMakefileArgs = ( "ABSTRACT" => "Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00", "AUTHOR" => "Aaron J Mackey , Jason Stajich ", "CONFIGURE_REQUIRES" => { "Devel::CheckBin" => 0, "ExtUtils::MakeMaker" => 0 }, "DISTNAME" => "Bio-Tools-Phylo-PAML", "EXE_FILES" => [ "bin/bp_pairwise_kaks" ], "LICENSE" => "perl", "MIN_PERL_VERSION" => "5.006", "NAME" => "Bio::Tools::Phylo::PAML", "PREREQ_PM" => { "Bio::Align::Utilities" => 0, "Bio::AlignIO" => 0, "Bio::AnalysisParserI" => 0, "Bio::AnalysisResultI" => 0, "Bio::LocatableSeq" => 0, "Bio::Matrix::PhylipDist" => 0, "Bio::PrimarySeq" => 0, "Bio::Root::IO" => 0, "Bio::Root::Root" => 0, "Bio::SeqIO" => 0, "Bio::Tools::Run::Alignment::Clustalw" => 0, "Bio::Tools::Run::Alignment::TCoffee" => 0, "Bio::Tools::Run::Phylo::PhyloBase" => 0, "Bio::Tools::Run::WrapperBase" => 0, "Bio::TreeIO" => 0, "Cwd" => 0, "File::Spec" => 0, "Getopt::Long" => 0, "IO::String" => 0, "base" => 0, "strict" => 0, "utf8" => 0, "vars" => 0, "warnings" => 0 }, "TEST_REQUIRES" => { "File::Spec" => 0, "IO::Handle" => 0, "IPC::Open3" => 0, "Test::More" => 0 }, "VERSION" => "1.7.3", "test" => { "TESTS" => "t/*.t" } ); my %FallbackPrereqs = ( "Bio::Align::Utilities" => 0, "Bio::AlignIO" => 0, "Bio::AnalysisParserI" => 0, "Bio::AnalysisResultI" => 0, "Bio::LocatableSeq" => 0, "Bio::Matrix::PhylipDist" => 0, "Bio::PrimarySeq" => 0, "Bio::Root::IO" => 0, "Bio::Root::Root" => 0, "Bio::SeqIO" => 0, "Bio::Tools::Run::Alignment::Clustalw" => 0, "Bio::Tools::Run::Alignment::TCoffee" => 0, "Bio::Tools::Run::Phylo::PhyloBase" => 0, "Bio::Tools::Run::WrapperBase" => 0, "Bio::TreeIO" => 0, "Cwd" => 0, "File::Spec" => 0, "Getopt::Long" => 0, "IO::Handle" => 0, "IO::String" => 0, "IPC::Open3" => 0, "Test::More" => 0, "base" => 0, "strict" => 0, "utf8" => 0, "vars" => 0, "warnings" => 0 ); unless ( eval { ExtUtils::MakeMaker->VERSION(6.63_03) } ) { delete $WriteMakefileArgs{TEST_REQUIRES}; delete $WriteMakefileArgs{BUILD_REQUIRES}; $WriteMakefileArgs{PREREQ_PM} = \%FallbackPrereqs; } delete $WriteMakefileArgs{CONFIGURE_REQUIRES} unless eval { ExtUtils::MakeMaker->VERSION(6.52) }; WriteMakefile(%WriteMakefileArgs); Bio-Tools-Phylo-PAML-1.7.3/bin/0000755000175000017500000000000013316145226016724 5ustar carandraugcarandraugBio-Tools-Phylo-PAML-1.7.3/bin/bp_pairwise_kaks0000644000175000017500000001632213316145226022170 0ustar carandraugcarandraug#!/usr/bin/env perl use utf8; use strict; use warnings; use Getopt::Long; use Bio::Align::Utilities qw(aa_to_dna_aln); use Bio::AlignIO; use Bio::SeqIO; use Bio::Tools::Run::Alignment::Clustalw; use Bio::Tools::Run::Alignment::TCoffee; use Bio::Tools::Run::Phylo::PAML::Codeml; use Bio::Tools::Run::Phylo::PAML::Yn00; # PODNAME: bp_pairwise_kaks # ABSTRACT: calculate pairwise Ka,Ks for a set of sequences # AUTHOR: Jason Stajich # OWNER: Jason Stajich # LICENSE: Perl_5 my $aln_prog = "clustalw"; my $kaks_prog = "codeml"; my $format = "fasta"; my $output; my $cdna; my $verbose; my $help; GetOptions( 'i|input:s' => \$cdna, 'o|output:s' => \$output, 'f|format:s' => \$format, 'msa:s' => \$aln_prog, 'kaks:s' => \$kaks_prog, 'v|verbose' => \$verbose, 'h|help' => \$help, ); if( $help ) { exec('perldoc',$0); exit(0); } $verbose = -1 unless $verbose; my ($aln_factory,$kaks_factory); if( $aln_prog =~ /clus/i ) { $aln_factory = Bio::Tools::Run::Alignment::Clustalw->new(-verbose => $verbose); } elsif( $aln_prog =~ /t\_?cof/i ) { $aln_factory = Bio::Tools::Run::Alignment::TCoffee->new(-verbose => $verbose); } else { warn("Did not provide either 'clustalw' or 'tcoffee' as alignment program names"); exit(0); } unless( $aln_factory->executable ) { warn("Could not find the executable for $aln_prog, make sure you have installed it and have either set ".uc($aln_prog)."DIR or it is in your PATH"); exit(0); } if( $kaks_prog =~ /yn00/i ) { $kaks_factory = Bio::Tools::Run::Phylo::PAML::Yn00->new(-verbose => $verbose); } elsif( $kaks_prog =~ /codeml/i ) { # change the parameters here if you want to tweak your Codeml running! $kaks_factory = Bio::Tools::Run::Phylo::PAML::Codeml->new (-verbose => $verbose, -params => { 'runmode' => -2, 'seqtype' => 1, } ); } unless ( $kaks_factory->executable ) { warn("Could not find the executable for $kaks_prog, make sure you have installed it and you have defined PAMLDIR or it is in your PATH"); exit(0); } unless ( $cdna && -f $cdna && -r $cdna && ! -z $cdna ) { warn("Did not specify a valid cDNA sequence file as input"); exit(0); } my $seqin = new Bio::SeqIO(-file => $cdna, -format => $format); my %seqs; my @prots; while( my $seq = $seqin->next_seq ) { $seqs{$seq->display_id} = $seq; my $protein = $seq->translate(); my $pseq = $protein->seq(); $pseq =~ s/\*$//; if( $pseq =~ /\*/ ) { warn("provided a cDNA (".$seq->display_id.") sequence with a stop codon, PAML will choke!"); exit(0); } # Tcoffee can't handle '*' $pseq =~ s/\*//g; $protein->seq($pseq); push @prots, $protein; } if( @prots < 2 ) { warn("Need at least 2 cDNA sequences to proceed"); exit(0); } local * OUT; if( $output ) { open(OUT, ">$output") || die("cannot open output $output for writing"); } else { *OUT = *STDOUT; } my $aa_aln = $aln_factory->align(\@prots); my $dna_aln = &aa_to_dna_aln($aa_aln, \%seqs); my @each = $dna_aln->each_seq(); $kaks_factory->alignment($dna_aln); my ($rc,$parser) = $kaks_factory->run(); if( $rc <= 0 ) { warn($kaks_factory->error_string,"\n"); exit; } my $result = $parser->next_result; if ($result->version =~ m/3\.15/) { warn("This script does not work with v3.15 of PAML! Please use 3.14 instead."); exit(0); } my $MLmatrix = $result->get_MLmatrix(); my @otus = $result->get_seqs(); my @pos = map { my $c= 1; foreach my $s ( @each ) { last if( $s->display_id eq $_->display_id ); $c++; } $c; } @otus; print OUT join("\t", qw(SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID)), "\n"; for( my $i = 0; $i < (scalar @otus -1) ; $i++) { for( my $j = $i+1; $j < (scalar @otus); $j++ ) { my $sub_aa_aln = $aa_aln->select_noncont($pos[$i],$pos[$j]); my $sub_dna_aln = $dna_aln->select_noncont($pos[$i],$pos[$j]); print OUT join("\t", $otus[$i]->display_id, $otus[$j]->display_id,$MLmatrix->[$i]->[$j]->{'dN'}, $MLmatrix->[$i]->[$j]->{'dS'}, $MLmatrix->[$i]->[$j]->{'omega'}, sprintf("%.2f",$sub_aa_aln->percentage_identity), sprintf("%.2f",$sub_dna_aln->percentage_identity), ), "\n"; } } __END__ =pod =encoding UTF-8 =head1 NAME bp_pairwise_kaks - calculate pairwise Ka,Ks for a set of sequences =head1 VERSION version 1.7.3 =head1 SYNOPSIS bp_pairwise_kaks.PLS -i INPUT-cDNA [-f FORMAT] [-o OUTPUT] \ [--msa tcoffee|clustal] [--kaks yn00|codeml] =head1 DESCRIPTION This script will take as input a dataset of cDNA sequences, verify that they contain no stop codons, align them in protein space, project the alignment back into cDNA, and estimate the Ka (non-synonymous) and Ks (synonymous) substitutions based on the Maximum Likelihood method of Yang with the PAML package. Often there are specific specific parameters you want to run when you are computing Ka/Ks ratios so consider this script a starting point and do not rely it on for every situation. =head1 OPTIONS =over 4 =item B<-i>, B<--input> The input file with the cDNA sequences. Must have at least two sequences, and be in a format that L is capable to read. In addition, if Bio::SeqIO is inable to automatically identify the format, the B<-f> option should be specified. Technically not an option, this is a required value. =item B<-f>, B<--format> Specify the format of INPUT-cDNA for L. =item B<-o>, B<--output> Specify the file for output. Defaults to STDOUT. =item B<--msa> Program used for alignment, either clustalw or tcoffee. Defaults to clustalw. =item B<--kaks> Program used for the Ka/Ks estimation, either codeml or yn00. Defaults to codeml. =item B<-v>, B<--verbose> Be verbose. =item B<-h>, B<--help> Print help text. =back =head1 FEEDBACK =head2 Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bio-tools-phylo-paml/issues =head1 AUTHOR Jason Stajich =head1 COPYRIGHT This software is copyright (c) by Jason Stajich . This software is available under the same terms as the perl 5 programming language system itself. =cut