debian/0000755000000000000000000000000012214301670007162 5ustar debian/watch0000644000000000000000000000010511237220540010207 0ustar version=3 ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-(.*).tar.gz debian/copyright0000644000000000000000000000442611775044354011141 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.tar.gz Disclaimer: This package is not part of the Debian operating system. The embassy-phylip source and binary Debian packages are part of the “non-free” area in the Debian archive. The packages in this area are not part of the Debian system, although they have been configured for use with Debian. We nevertheless support the use of the seaview source and binary Debian packages and provide infrastructure for non-free packages (such as our bug tracking system and mailing lists). The licence of PHYLIPNEW does not forbid Debian from using autobuilders to create binary packages. Comment: It was confirmed on the EMBOSS User mailing list that the COPYING file (GNU GPL) is there by error and the Phylip copyright file applies on all the package. http://lists.open-bio.org/pipermail/emboss/2009-August/003713.html Files: * Copyright: © 1993-2004 by the University of Washington. License: Phylip Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe. Permission is granted to copy and use this program provided no fee is charged for it and provided that this copyright notice is not removed. Files: doc/* emboss-doc/* Copyright: 1986-2002 by the University of Washington. License: Phylip-doc Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed. Files: debian/* Copyright: 2009–2011 Charles Plessy License: BOLA-1.0 This work is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this work. . To all effects and purposes, this work is to be considered Public Domain. . . However, if you want to be "buena onda", you should: . 1. Not take credit for it, and give proper recognition to the authors. 2. Share your modifications, so everybody benefits from them. 3. Do something nice for the authors. 4. Help someone who needs it. 5. Don't waste. Anything, but specially energy that comes from natural non-renewable resources. 6. Be tolerant. Everything that's good in nature comes from cooperation. debian/manpages/0000755000000000000000000000000012214275755010773 5ustar debian/manpages/fcontml.1e0000644000000000000000000000724511434420167012664 0ustar '\" t .\" Title: FCONTML .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FCONTML" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fcontml \- Gene frequency and continuous character Maximum Likelihood .SH "SYNOPSIS" .HP \w'\fBfcontml\fR\ 'u \fBfcontml\fR \fB\-infile\ \fR\fB\fIfrequencies\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-datatype\ \fR\fB\fIlist\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfcontml\fR\ 'u \fBfcontml\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfcontml\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Gene frequencies" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIfrequencies\fR .RS 4 File containing one or more sets of data .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .SS "Additional section" .PP \fB\-datatype\fR \fIlist\fR .RS 4 Default value: g .RE .PP \fB\-lengths\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-njumble\fR \fIinteger\fR .RS 4 .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-global\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fcontml is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fdnacomp.1e0000644000000000000000000000722311434420167013005 0ustar '\" t .\" Title: FDNACOMP .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FDNACOMP" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fdnacomp \- DNA compatibility algorithm .SH "SYNOPSIS" .HP \w'\fBfdnacomp\fR\ 'u \fBfdnacomp\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR \fB\-weights\ \fR\fB\fIproperties\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfdnacomp\fR\ 'u \fBfdnacomp\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfdnacomp\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqsetall\fR .RS 4 File containing one or more sequence alignments .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .PP \fB\-njumble\fR \fIinteger\fR .RS 4 .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-stepbox\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-ancseq\fR \fIboolean\fR .RS 4 Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fdnacomp is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/frestml.1e0000644000000000000000000000773311434420167012700 0ustar '\" t .\" Title: FRESTML .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FRESTML" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" frestml \- Restriction site maximum Likelihood method .SH "SYNOPSIS" .HP \w'\fBfrestml\fR\ 'u \fBfrestml\fR \fB\-data\ \fR\fB\fIdiscretestates\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-njumble\ \fR\fB\fIinteger\fR\fR] \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-allsites\ \fR\fB\fIboolean\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR [\fB\-sitelength\ \fR\fB\fIinteger\fR\fR] \fB\-global\ \fR\fB\fIboolean\fR\fR \fB\-rough\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfrestml\fR\ 'u \fBfrestml\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfrestml\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-data\fR \fIdiscretestates\fR .RS 4 File containing one or more sets of restriction data .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 Weights file .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .SS "Additional section" .PP \fB\-njumble\fR \fIinteger\fR .RS 4 .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .PP \fB\-allsites\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-lengths\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-sitelength\fR \fIinteger\fR .RS 4 Default value: 6 .RE .PP \fB\-global\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-rough\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP frestml is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fdnamove.1e0000644000000000000000000000650411434420167013016 0ustar '\" t .\" Title: FDNAMOVE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FDNAMOVE" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fdnamove \- Interactive DNA parsimony .SH "SYNOPSIS" .HP \w'\fBfdnamove\fR\ 'u \fBfdnamove\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-initialtree\ \fR\fB\fIlist\fR\fR] [\fB\-screenwidth\ \fR\fB\fIinteger\fR\fR] [\fB\-screenlines\ \fR\fB\fIinteger\fR\fR] [\fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBfdnamove\fR\ 'u \fBfdnamove\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfdnamove\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqsetall\fR .RS 4 .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 Weights file \- ignore sites with weight zero .RE .SS "Additional section" .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .PP \fB\-thresh\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-threshold\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-initialtree\fR \fIlist\fR .RS 4 Default value: Arbitary .RE .PP \fB\-screenwidth\fR \fIinteger\fR .RS 4 Default value: 80 .RE .PP \fB\-screenlines\fR \fIinteger\fR .RS 4 Default value: 24 .RE .SS "Output section" .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fdnamove is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ftreedist.1e0000644000000000000000000000605311434420167013207 0ustar '\" t .\" Title: FTREEDIST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FTREEDIST" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ftreedist \- Distances between trees .SH "SYNOPSIS" .HP \w'\fBftreedist\fR\ 'u \fBftreedist\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-dtype\ \fR\fB\fIlist\fR\fR] [\fB\-pairing\ \fR\fB\fIlist\fR\fR] [\fB\-style\ \fR\fB\fIlist\fR\fR] [\fB\-noroot\ \fR\fB\fIboolean\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBftreedist\fR\ 'u \fBftreedist\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBftreedist\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Consensus" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .SS "Additional section" .PP \fB\-dtype\fR \fIlist\fR .RS 4 Default value: b .RE .PP \fB\-pairing\fR \fIlist\fR .RS 4 Default value: a .RE .PP \fB\-style\fR \fIlist\fR .RS 4 Default value: v .RE .PP \fB\-noroot\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ftreedist is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fseqbootall.1e0000644000000000000000000001103611434420167013526 0ustar '\" t .\" Title: FSEQBOOTALL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FSEQBOOTALL" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fseqbootall \- Bootstrapped sequences algorithm .SH "SYNOPSIS" .HP \w'\fBfseqbootall\fR\ 'u \fBfseqbootall\fR \fB\-infilesequences\ \fR\fB\fIseqset\fR\fR [\fB\-categories\ \fR\fB\fIproperties\fR\fR] [\fB\-mixfile\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-factorfile\ \fR\fB\fIproperties\fR\fR] \fB\-datatype\ \fR\fB\fIlist\fR\fR \fB\-test\ \fR\fB\fIlist\fR\fR \fB\-regular\ \fR\fB\fItoggle\fR\fR \fB\-fracsample\ \fR\fB\fIfloat\fR\fR \fB\-rewriteformat\ \fR\fB\fIlist\fR\fR \fB\-seqtype\ \fR\fB\fIlist\fR\fR \fB\-morphseqtype\ \fR\fB\fIlist\fR\fR \fB\-blocksize\ \fR\fB\fIinteger\fR\fR \fB\-reps\ \fR\fB\fIinteger\fR\fR \fB\-justweights\ \fR\fB\fIlist\fR\fR \fB\-enzymes\ \fR\fB\fIboolean\fR\fR \fB\-all\ \fR\fB\fIboolean\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfseqbootall\fR\ 'u \fBfseqbootall\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfseqbootall\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infilesequences\fR \fIseqset\fR .RS 4 .RE .PP \fB\-categories\fR \fIproperties\fR .RS 4 .RE .PP \fB\-mixfile\fR \fIproperties\fR .RS 4 .RE .PP \fB\-ancfile\fR \fIproperties\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 Weights file .RE .PP \fB\-factorfile\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-datatype\fR \fIlist\fR .RS 4 Default value: s .RE .PP \fB\-test\fR \fIlist\fR .RS 4 Default value: b .RE .PP \fB\-regular\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-fracsample\fR \fIfloat\fR .RS 4 Default value: 100\&.0 .RE .PP \fB\-rewriteformat\fR \fIlist\fR .RS 4 Default value: p .RE .PP \fB\-seqtype\fR \fIlist\fR .RS 4 Default value: d .RE .PP \fB\-morphseqtype\fR \fIlist\fR .RS 4 Default value: p .RE .PP \fB\-blocksize\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-reps\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-justweights\fR \fIlist\fR .RS 4 Default value: d .RE .PP \fB\-enzymes\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-all\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-dotdiff\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fseqbootall is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fseqboot.1e0000644000000000000000000000754411434420167013046 0ustar '\" t .\" Title: FSEQBOOT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FSEQBOOT" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fseqboot \- Bootstrapped sequences algorithm .SH "SYNOPSIS" .HP \w'\fBfseqboot\fR\ 'u \fBfseqboot\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR [\fB\-categories\ \fR\fB\fIproperties\fR\fR] [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-test\ \fR\fB\fIlist\fR\fR \fB\-regular\ \fR\fB\fItoggle\fR\fR \fB\-fracsample\ \fR\fB\fIfloat\fR\fR \fB\-rewriteformat\ \fR\fB\fIlist\fR\fR \fB\-seqtype\ \fR\fB\fIlist\fR\fR \fB\-blocksize\ \fR\fB\fIinteger\fR\fR \fB\-reps\ \fR\fB\fIinteger\fR\fR \fB\-justweights\ \fR\fB\fIlist\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfseqboot\fR\ 'u \fBfseqboot\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfseqboot\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqset\fR .RS 4 .RE .PP \fB\-categories\fR \fIproperties\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 Weights file .RE .SS "Additional section" .PP \fB\-test\fR \fIlist\fR .RS 4 Default value: b .RE .PP \fB\-regular\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-fracsample\fR \fIfloat\fR .RS 4 Default value: 100\&.0 .RE .PP \fB\-rewriteformat\fR \fIlist\fR .RS 4 Default value: p .RE .PP \fB\-seqtype\fR \fIlist\fR .RS 4 Default value: d .RE .PP \fB\-blocksize\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-reps\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-justweights\fR \fIlist\fR .RS 4 Default value: d .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-dotdiff\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fseqboot is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fproml.1e0000644000000000000000000001254011434420167012513 0ustar '\" t .\" Title: FPROML .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FPROML" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fproml \- Protein phylogeny by maximum likelihood .SH "SYNOPSIS" .HP \w'\fBfproml\fR\ 'u \fBfproml\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-ncategories\ \fR\fB\fIinteger\fR\fR] \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR [\fB\-model\ \fR\fB\fIlist\fR\fR] [\fB\-gamma\ \fR\fB\fIlist\fR\fR] \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ngammacat\ \fR\fB\fIinteger\fR\fR \fB\-invarcoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ninvarcat\ \fR\fB\fIinteger\fR\fR \fB\-invarfrac\ \fR\fB\fIfloat\fR\fR \fB\-nhmmcategories\ \fR\fB\fIinteger\fR\fR \fB\-hmmrates\ \fR\fB\fIarray\fR\fR \fB\-hmmprobabilities\ \fR\fB\fIarray\fR\fR \fB\-adjsite\ \fR\fB\fIboolean\fR\fR \fB\-lambda\ \fR\fB\fIfloat\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-rough\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-hypstate\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfproml\fR\ 'u \fBfproml\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfproml\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqsetall\fR .RS 4 File containing one or more sequence alignments .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .PP \fB\-ncategories\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-rate\fR \fIarray\fR .RS 4 .RE .PP \fB\-categories\fR \fIproperties\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 Weights file .RE .SS "Additional section" .PP \fB\-lengths\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-model\fR \fIlist\fR .RS 4 Default value: Jones\-Taylor\-Thornton .RE .PP \fB\-gamma\fR \fIlist\fR .RS 4 Default value: Constant rate .RE .PP \fB\-gammacoefficient\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-ngammacat\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-invarcoefficient\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-ninvarcat\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-invarfrac\fR \fIfloat\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-nhmmcategories\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-hmmrates\fR \fIarray\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-hmmprobabilities\fR \fIarray\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-adjsite\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-lambda\fR \fIfloat\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-njumble\fR \fIinteger\fR .RS 4 .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-global\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .PP \fB\-rough\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-hypstate\fR \fIboolean\fR .RS 4 Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fproml is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/frestdist.1e0000644000000000000000000000676211434420167013234 0ustar '\" t .\" Title: FRESTDIST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FRESTDIST" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" frestdist \- Distance matrix from restriction sites or fragments .SH "SYNOPSIS" .HP \w'\fBfrestdist\fR\ 'u \fBfrestdist\fR \fB\-data\ \fR\fB\fIdiscretestates\fR\fR [\fB\-restsites\ \fR\fB\fIboolean\fR\fR] [\fB\-neili\ \fR\fB\fIboolean\fR\fR] \fB\-gamma\ \fR\fB\fIboolean\fR\fR \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR [\fB\-ttratio\ \fR\fB\fIfloat\fR\fR] [\fB\-sitelength\ \fR\fB\fIinteger\fR\fR] [\fB\-lower\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfrestdist\fR\ 'u \fBfrestdist\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfrestdist\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-data\fR \fIdiscretestates\fR .RS 4 File containing one or more sets of restriction data .RE .SS "Additional section" .PP \fB\-restsites\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-neili\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-gamma\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-gammacoefficient\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-ttratio\fR \fIfloat\fR .RS 4 Default value: 2\&.0 .RE .PP \fB\-sitelength\fR \fIinteger\fR .RS 4 Default value: 6 .RE .PP \fB\-lower\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP frestdist is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fpromlk.1e0000644000000000000000000001236011434420167012666 0ustar '\" t .\" Title: FPROMLK .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FPROMLK" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fpromlk \- Protein phylogeny by maximum likelihood .SH "SYNOPSIS" .HP \w'\fBfpromlk\fR\ 'u \fBfpromlk\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-ncategories\ \fR\fB\fIinteger\fR\fR] \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR [\fB\-model\ \fR\fB\fIlist\fR\fR] [\fB\-gamma\ \fR\fB\fIlist\fR\fR] \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ngammacat\ \fR\fB\fIinteger\fR\fR \fB\-invarcoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ninvarcat\ \fR\fB\fIinteger\fR\fR \fB\-invarfrac\ \fR\fB\fIfloat\fR\fR \fB\-nhmmcategories\ \fR\fB\fIinteger\fR\fR \fB\-hmmrates\ \fR\fB\fIarray\fR\fR \fB\-hmmprobabilities\ \fR\fB\fIarray\fR\fR \fB\-adjsite\ \fR\fB\fIboolean\fR\fR \fB\-lambda\ \fR\fB\fIfloat\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-hypstate\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfpromlk\fR\ 'u \fBfpromlk\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfpromlk\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqsetall\fR .RS 4 File containing one or more sequence alignments .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .PP \fB\-ncategories\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-rate\fR \fIarray\fR .RS 4 .RE .PP \fB\-categories\fR \fIproperties\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-lengths\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-model\fR \fIlist\fR .RS 4 Default value: Jones\-Taylor\-Thornton .RE .PP \fB\-gamma\fR \fIlist\fR .RS 4 Default value: n .RE .PP \fB\-gammacoefficient\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-ngammacat\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-invarcoefficient\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-ninvarcat\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-invarfrac\fR \fIfloat\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-nhmmcategories\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-hmmrates\fR \fIarray\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-hmmprobabilities\fR \fIarray\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-adjsite\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-lambda\fR \fIfloat\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-njumble\fR \fIinteger\fR .RS 4 .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-global\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-hypstate\fR \fIboolean\fR .RS 4 Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fpromlk is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fkitsch.1e0000644000000000000000000000744111434420167012653 0ustar '\" t .\" Title: FKITSCH .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FKITSCH" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fkitsch \- Fitch\-Margoliash method with contemporary tips .SH "SYNOPSIS" .HP \w'\fBfkitsch\fR\ 'u \fBfkitsch\fR \fB\-datafile\ \fR\fB\fIdistances\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-matrixtype\ \fR\fB\fIlist\fR\fR] [\fB\-minev\ \fR\fB\fIboolean\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-power\ \fR\fB\fIfloat\fR\fR] [\fB\-negallowed\ \fR\fB\fIboolean\fR\fR] [\fB\-replicates\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfkitsch\fR\ 'u \fBfkitsch\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfkitsch\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Distance matrix" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-datafile\fR \fIdistances\fR .RS 4 File containing one or more distance matrices .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .SS "Additional section" .PP \fB\-matrixtype\fR \fIlist\fR .RS 4 Default value: s .RE .PP \fB\-minev\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-njumble\fR \fIinteger\fR .RS 4 .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-power\fR \fIfloat\fR .RS 4 Default value: 2\&.0 .RE .PP \fB\-negallowed\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-replicates\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fkitsch is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fdnadist.1e0000644000000000000000000001022211434420167013003 0ustar '\" t .\" Title: FDNADIST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FDNADIST" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fdnadist \- Nucleic acid sequence Distance Matrix program .SH "SYNOPSIS" .HP \w'\fBfdnadist\fR\ 'u \fBfdnadist\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-method\ \fR\fB\fIlist\fR\fR \fB\-gamma\ \fR\fB\fIlist\fR\fR \fB\-ncategories\ \fR\fB\fIinteger\fR\fR \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-invarfrac\ \fR\fB\fIfloat\fR\fR \fB\-ttratio\ \fR\fB\fIfloat\fR\fR \fB\-freqsfrom\ \fR\fB\fItoggle\fR\fR \fB\-basefreq\ \fR\fB\fIarray\fR\fR [\fB\-lower\ \fR\fB\fIboolean\fR\fR] [\fB\-humanreadable\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfdnadist\fR\ 'u \fBfdnadist\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfdnadist\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqsetall\fR .RS 4 File containing one or more sequence alignments .RE .PP \fB\-method\fR \fIlist\fR .RS 4 Default value: F84 distance model .RE .PP \fB\-gamma\fR \fIlist\fR .RS 4 Default value: No distribution parameters used .RE .PP \fB\-ncategories\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-rate\fR \fIarray\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-categories\fR \fIproperties\fR .RS 4 File of substitution rate categories .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-gammacoefficient\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-invarfrac\fR \fIfloat\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-ttratio\fR \fIfloat\fR .RS 4 Default value: 2\&.0 .RE .PP \fB\-freqsfrom\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-basefreq\fR \fIarray\fR .RS 4 Default value: 0\&.25 0\&.25 0\&.25 0\&.25 .RE .PP \fB\-lower\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-humanreadable\fR \fIboolean\fR .RS 4 Default value: @($(method)==s?Y:N) .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fdnadist is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ffreqboot.1e0000644000000000000000000000713211434420167013204 0ustar '\" t .\" Title: FFREQBOOT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FFREQBOOT" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ffreqboot \- Bootstrapped genetic frequencies algorithm .SH "SYNOPSIS" .HP \w'\fBffreqboot\fR\ 'u \fBffreqboot\fR \fB\-infile\ \fR\fB\fIfrequencies\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-test\ \fR\fB\fIlist\fR\fR \fB\-regular\ \fR\fB\fItoggle\fR\fR \fB\-fracsample\ \fR\fB\fIfloat\fR\fR \fB\-blocksize\ \fR\fB\fIinteger\fR\fR \fB\-reps\ \fR\fB\fIinteger\fR\fR \fB\-justweights\ \fR\fB\fIlist\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBffreqboot\fR\ 'u \fBffreqboot\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBffreqboot\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIfrequencies\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 Weights file .RE .SS "Additional section" .PP \fB\-test\fR \fIlist\fR .RS 4 Default value: b .RE .PP \fB\-regular\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-fracsample\fR \fIfloat\fR .RS 4 Default value: 100\&.0 .RE .PP \fB\-blocksize\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-reps\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-justweights\fR \fIlist\fR .RS 4 Default value: d .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-dotdiff\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ffreqboot is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fdnamlk.1e0000644000000000000000000001261211434420167012630 0ustar '\" t .\" Title: FDNAMLK .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FDNAMLK" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fdnamlk \- Estimates nucleotide phylogeny by maximum likelihood .SH "SYNOPSIS" .HP \w'\fBfdnamlk\fR\ 'u \fBfdnamlk\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-ncategories\ \fR\fB\fIinteger\fR\fR] \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ttratio\ \fR\fB\fIfloat\fR\fR] [\fB\-freqsfrom\ \fR\fB\fItoggle\fR\fR] \fB\-basefreq\ \fR\fB\fIarray\fR\fR [\fB\-gamma\ \fR\fB\fIlist\fR\fR] \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ngammacat\ \fR\fB\fIinteger\fR\fR \fB\-invarcoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ninvarcat\ \fR\fB\fIinteger\fR\fR \fB\-invarfrac\ \fR\fB\fIfloat\fR\fR \fB\-nhmmcategories\ \fR\fB\fIinteger\fR\fR \fB\-hmmrates\ \fR\fB\fIarray\fR\fR \fB\-hmmprobabilities\ \fR\fB\fIarray\fR\fR \fB\-adjsite\ \fR\fB\fIboolean\fR\fR \fB\-lambda\ \fR\fB\fIfloat\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR \fB\-lengths\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-hypstate\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfdnamlk\fR\ 'u \fBfdnamlk\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfdnamlk\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqsetall\fR .RS 4 File containing one or more sequence alignments .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .PP \fB\-ncategories\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-rate\fR \fIarray\fR .RS 4 .RE .PP \fB\-categories\fR \fIproperties\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-ttratio\fR \fIfloat\fR .RS 4 Default value: 2\&.0 .RE .PP \fB\-freqsfrom\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-basefreq\fR \fIarray\fR .RS 4 Default value: 0\&.25 0\&.25 0\&.25 0\&.25 .RE .PP \fB\-gamma\fR \fIlist\fR .RS 4 Default value: Constant rate .RE .PP \fB\-gammacoefficient\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-ngammacat\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-invarcoefficient\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-ninvarcat\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-invarfrac\fR \fIfloat\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-nhmmcategories\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-hmmrates\fR \fIarray\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-hmmprobabilities\fR \fIarray\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-adjsite\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-lambda\fR \fIfloat\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-njumble\fR \fIinteger\fR .RS 4 .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-global\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-lengths\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-hypstate\fR \fIboolean\fR .RS 4 Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fdnamlk is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fdiscboot.1e0000644000000000000000000001033111434420167013164 0ustar '\" t .\" Title: FDISCBOOT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FDISCBOOT" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fdiscboot \- Bootstrapped discrete sites algorithm .SH "SYNOPSIS" .HP \w'\fBfdiscboot\fR\ 'u \fBfdiscboot\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR [\fB\-mixfile\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-factorfile\ \fR\fB\fIproperties\fR\fR] \fB\-test\ \fR\fB\fIlist\fR\fR \fB\-regular\ \fR\fB\fItoggle\fR\fR \fB\-fracsample\ \fR\fB\fIfloat\fR\fR \fB\-morphseqtype\ \fR\fB\fIlist\fR\fR \fB\-blocksize\ \fR\fB\fIinteger\fR\fR \fB\-reps\ \fR\fB\fIinteger\fR\fR \fB\-justweights\ \fR\fB\fIlist\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outancfile\ \fR\fB\fIoutfile\fR\fR \fB\-outmixfile\ \fR\fB\fIoutfile\fR\fR \fB\-outfactfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfdiscboot\fR\ 'u \fBfdiscboot\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfdiscboot\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIdiscretestates\fR .RS 4 .RE .PP \fB\-mixfile\fR \fIproperties\fR .RS 4 .RE .PP \fB\-ancfile\fR \fIproperties\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 Weights file .RE .PP \fB\-factorfile\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-test\fR \fIlist\fR .RS 4 Default value: b .RE .PP \fB\-regular\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-fracsample\fR \fIfloat\fR .RS 4 Default value: 100\&.0 .RE .PP \fB\-morphseqtype\fR \fIlist\fR .RS 4 Default value: p .RE .PP \fB\-blocksize\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-reps\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-justweights\fR \fIlist\fR .RS 4 Default value: d .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-outancfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-outmixfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-outfactfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-dotdiff\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fdiscboot is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fdolpenny.1e0000644000000000000000000000777411434420167013227 0ustar '\" t .\" Title: FDOLPENNY .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FDOLPENNY" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fdolpenny \- Penny algorithm Dollo or polymorphism .SH "SYNOPSIS" .HP \w'\fBfdolpenny\fR\ 'u \fBfdolpenny\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-howmany\ \fR\fB\fIinteger\fR\fR] [\fB\-howoften\ \fR\fB\fIinteger\fR\fR] [\fB\-simple\ \fR\fB\fIboolean\fR\fR] [\fB\-method\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfdolpenny\fR\ 'u \fBfdolpenny\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfdolpenny\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIdiscretestates\fR .RS 4 File containing one or more data sets .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 .RE .PP \fB\-ancfile\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-thresh\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-threshold\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-howmany\fR \fIinteger\fR .RS 4 Default value: 1000 .RE .PP \fB\-howoften\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-simple\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-method\fR \fIlist\fR .RS 4 Default value: d .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-ancseq\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-stepbox\fR \fIboolean\fR .RS 4 Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fdolpenny is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fmix.1e0000644000000000000000000000777011434420167012170 0ustar '\" t .\" Title: FMIX .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FMIX" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fmix \- Mixed parsimony algorithm .SH "SYNOPSIS" .HP \w'\fBfmix\fR\ 'u \fBfmix\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-mixfile\ \fR\fB\fIproperties\fR\fR] \fB\-method\ \fR\fB\fIlist\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfmix\fR\ 'u \fBfmix\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfmix\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIdiscretestates\fR .RS 4 File containing one or more data sets .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 .RE .PP \fB\-ancfile\fR \fIproperties\fR .RS 4 .RE .PP \fB\-mixfile\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-method\fR \fIlist\fR .RS 4 Default value: Wagner .RE .PP \fB\-njumble\fR \fIinteger\fR .RS 4 .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .PP \fB\-threshold\fR \fIfloat\fR .RS 4 Default value: $(infile\&.discretesize) .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-ancseq\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-stepbox\fR \fIboolean\fR .RS 4 Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fmix is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fconsense.1e0000644000000000000000000000654711434420167013211 0ustar '\" t .\" Title: FCONSENSE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FCONSENSE" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fconsense \- Majority\-rule and strict consensus tree .SH "SYNOPSIS" .HP \w'\fBfconsense\fR\ 'u \fBfconsense\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-method\ \fR\fB\fIlist\fR\fR] \fB\-mlfrac\ \fR\fB\fIfloat\fR\fR [\fB\-root\ \fR\fB\fItoggle\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-prntsets\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfconsense\fR\ 'u \fBfconsense\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfconsense\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Consensus" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .SS "Additional section" .PP \fB\-method\fR \fIlist\fR .RS 4 Default value: mre .RE .PP \fB\-mlfrac\fR \fIfloat\fR .RS 4 Default value: 0\&.5 .RE .PP \fB\-root\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-prntsets\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fconsense is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fdnapenny.1e0000644000000000000000000000762311434420167013204 0ustar '\" t .\" Title: FDNAPENNY .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FDNAPENNY" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fdnapenny \- Penny algorithm for DNA .SH "SYNOPSIS" .HP \w'\fBfdnapenny\fR\ 'u \fBfdnapenny\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-howoften\ \fR\fB\fIinteger\fR\fR] [\fB\-howmany\ \fR\fB\fIinteger\fR\fR] [\fB\-simple\ \fR\fB\fIboolean\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfdnapenny\fR\ 'u \fBfdnapenny\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfdnapenny\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqsetall\fR .RS 4 File containing one or more sequence alignments .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-howoften\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-howmany\fR \fIinteger\fR .RS 4 Default value: 1000 .RE .PP \fB\-simple\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .PP \fB\-thresh\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-threshold\fR \fIfloat\fR .RS 4 Default value: 1\&.0 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-stepbox\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-ancseq\fR \fIboolean\fR .RS 4 Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fdnapenny is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fdnainvar.1e0000644000000000000000000000623311434420167013166 0ustar '\" t .\" Title: FDNAINVAR .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FDNAINVAR" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fdnainvar \- Nucleic acid sequence Invariants method .SH "SYNOPSIS" .HP \w'\fBfdnainvar\fR\ 'u \fBfdnainvar\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-weights\ \fR\fB\fIproperties\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-printpattern\ \fR\fB\fIboolean\fR\fR] [\fB\-printinvariant\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfdnainvar\fR\ 'u \fBfdnainvar\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfdnainvar\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqsetall\fR .RS 4 File containing one or more sequence alignments .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-dotdiff\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-printpattern\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-printinvariant\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fdnainvar is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ffitch.1e0000644000000000000000000001006111434420167012453 0ustar '\" t .\" Title: FFITCH .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FFITCH" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ffitch \- Fitch\-Margoliash and Least\-Squares Distance Methods .SH "SYNOPSIS" .HP \w'\fBffitch\fR\ 'u \fBffitch\fR \fB\-datafile\ \fR\fB\fIdistances\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-matrixtype\ \fR\fB\fIlist\fR\fR] [\fB\-minev\ \fR\fB\fIboolean\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-power\ \fR\fB\fIfloat\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR \fB\-negallowed\ \fR\fB\fIboolean\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR [\fB\-replicates\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBffitch\fR\ 'u \fBffitch\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBffitch\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Distance matrix" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-datafile\fR \fIdistances\fR .RS 4 File containing one or more distance matrices .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .SS "Additional section" .PP \fB\-matrixtype\fR \fIlist\fR .RS 4 Default value: s .RE .PP \fB\-minev\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-njumble\fR \fIinteger\fR .RS 4 .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .PP \fB\-power\fR \fIfloat\fR .RS 4 Default value: 2\&.0 .RE .PP \fB\-lengths\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-negallowed\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-global\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-replicates\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ffitch is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fneighbor.1e0000644000000000000000000000712311434420167013160 0ustar '\" t .\" Title: FNEIGHBOR .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FNEIGHBOR" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fneighbor \- Phylogenies from distance matrix by N\-J or UPGMA method .SH "SYNOPSIS" .HP \w'\fBfneighbor\fR\ 'u \fBfneighbor\fR \fB\-datafile\ \fR\fB\fIdistances\fR\fR [\fB\-matrixtype\ \fR\fB\fIlist\fR\fR] [\fB\-treetype\ \fR\fB\fIlist\fR\fR] \fB\-outgrno\ \fR\fB\fIinteger\fR\fR [\fB\-jumble\ \fR\fB\fItoggle\fR\fR] \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-replicates\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfneighbor\fR\ 'u \fBfneighbor\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfneighbor\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Distance matrix" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-datafile\fR \fIdistances\fR .RS 4 .RE .SS "Additional section" .PP \fB\-matrixtype\fR \fIlist\fR .RS 4 Default value: s .RE .PP \fB\-treetype\fR \fIlist\fR .RS 4 Default value: n .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .PP \fB\-jumble\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-replicates\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fneighbor is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fdrawtree.1e0000644000000000000000000001130111434420167013171 0ustar '\" t .\" Title: FDRAWTREE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FDRAWTREE" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fdrawtree \- Plots an unrooted tree diagram .SH "SYNOPSIS" .HP \w'\fBfdrawtree\fR\ 'u \fBfdrawtree\fR \fB\-fontfile\ \fR\fB\fIstring\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR \fB\-plotfile\ \fR\fB\fIoutfile\fR\fR [\fB\-plotter\ \fR\fB\fIlist\fR\fR] [\fB\-previewer\ \fR\fB\fIlist\fR\fR] [\fB\-iterate\ \fR\fB\fIlist\fR\fR] [\fB\-lengths\ \fR\fB\fIboolean\fR\fR] [\fB\-labeldirection\ \fR\fB\fIlist\fR\fR] [\fB\-treeangle\ \fR\fB\fIfloat\fR\fR] [\fB\-arc\ \fR\fB\fIfloat\fR\fR] \fB\-labelrotation\ \fR\fB\fIfloat\fR\fR [\fB\-rescaled\ \fR\fB\fItoggle\fR\fR] \fB\-bscale\ \fR\fB\fIfloat\fR\fR [\fB\-treedepth\ \fR\fB\fIfloat\fR\fR] \fB\-xmargin\ \fR\fB\fIfloat\fR\fR \fB\-ymargin\ \fR\fB\fIfloat\fR\fR \fB\-xrayshade\ \fR\fB\fIfloat\fR\fR \fB\-yrayshade\ \fR\fB\fIfloat\fR\fR [\fB\-paperx\ \fR\fB\fIfloat\fR\fR] [\fB\-papery\ \fR\fB\fIfloat\fR\fR] [\fB\-pagesheight\ \fR\fB\fIfloat\fR\fR] [\fB\-pageswidth\ \fR\fB\fIfloat\fR\fR] [\fB\-hpmargin\ \fR\fB\fIfloat\fR\fR] [\fB\-vpmargin\ \fR\fB\fIfloat\fR\fR] .HP \w'\fBfdrawtree\fR\ 'u \fBfdrawtree\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfdrawtree\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Tree drawing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-fontfile\fR \fIstring\fR .RS 4 Default value: font1 .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .SS "Additional section" .SS "Output section" .PP \fB\-plotfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-plotter\fR \fIlist\fR .RS 4 Default value: l .RE .PP \fB\-previewer\fR \fIlist\fR .RS 4 Default value: x .RE .PP \fB\-iterate\fR \fIlist\fR .RS 4 Default value: e .RE .PP \fB\-lengths\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-labeldirection\fR \fIlist\fR .RS 4 Default value: m .RE .PP \fB\-treeangle\fR \fIfloat\fR .RS 4 Default value: 90\&.0 .RE .PP \fB\-arc\fR \fIfloat\fR .RS 4 Default value: 360 .RE .PP \fB\-labelrotation\fR \fIfloat\fR .RS 4 Default value: 90\&.0 .RE .PP \fB\-rescaled\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-bscale\fR \fIfloat\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-treedepth\fR \fIfloat\fR .RS 4 Default value: 0\&.53 .RE .PP \fB\-xmargin\fR \fIfloat\fR .RS 4 Default value: 1\&.65 .RE .PP \fB\-ymargin\fR \fIfloat\fR .RS 4 Default value: 2\&.16 .RE .PP \fB\-xrayshade\fR \fIfloat\fR .RS 4 Default value: 1\&.65 .RE .PP \fB\-yrayshade\fR \fIfloat\fR .RS 4 Default value: 2\&.16 .RE .PP \fB\-paperx\fR \fIfloat\fR .RS 4 Default value: 20\&.63750 .RE .PP \fB\-papery\fR \fIfloat\fR .RS 4 Default value: 26\&.98750 .RE .PP \fB\-pagesheight\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-pageswidth\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-hpmargin\fR \fIfloat\fR .RS 4 Default value: 0\&.41275 .RE .PP \fB\-vpmargin\fR \fIfloat\fR .RS 4 Default value: 0\&.53975 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fdrawtree is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fcontrast.1e0000644000000000000000000000635311434420167013224 0ustar '\" t .\" Title: FCONTRAST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FCONTRAST" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fcontrast \- Continuous character Contrasts .SH "SYNOPSIS" .HP \w'\fBfcontrast\fR\ 'u \fBfcontrast\fR \fB\-infile\ \fR\fB\fIfrequencies\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-varywithin\ \fR\fB\fIboolean\fR\fR] \fB\-reg\ \fR\fB\fIboolean\fR\fR \fB\-writecont\ \fR\fB\fIboolean\fR\fR \fB\-nophylo\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfcontrast\fR\ 'u \fBfcontrast\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfcontrast\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Continuous characters" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIfrequencies\fR .RS 4 File containing one or more sets of data .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .SS "Additional section" .PP \fB\-varywithin\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-reg\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-writecont\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-nophylo\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fcontrast is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fdolmove.1e0000644000000000000000000000702511434420167013031 0ustar '\" t .\" Title: FDOLMOVE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FDOLMOVE" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fdolmove \- Interactive Dollo or Polymorphism Parsimony .SH "SYNOPSIS" .HP \w'\fBfdolmove\fR\ 'u \fBfdolmove\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-factorfile\ \fR\fB\fIproperties\fR\fR] [\fB\-method\ \fR\fB\fIlist\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-initialtree\ \fR\fB\fIlist\fR\fR] [\fB\-screenwidth\ \fR\fB\fIinteger\fR\fR] [\fB\-screenlines\ \fR\fB\fIinteger\fR\fR] [\fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBfdolmove\fR\ 'u \fBfdolmove\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfdolmove\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIdiscretestates\fR .RS 4 File containing data set .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 Weights file .RE .PP \fB\-ancfile\fR \fIproperties\fR .RS 4 .RE .PP \fB\-factorfile\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-method\fR \fIlist\fR .RS 4 Default value: d .RE .PP \fB\-thresh\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-threshold\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-initialtree\fR \fIlist\fR .RS 4 Default value: Arbitary .RE .PP \fB\-screenwidth\fR \fIinteger\fR .RS 4 Default value: 80 .RE .PP \fB\-screenlines\fR \fIinteger\fR .RS 4 Default value: 24 .RE .SS "Output section" .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fdolmove is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fdollop.1e0000644000000000000000000000756511434420167012666 0ustar '\" t .\" Title: FDOLLOP .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FDOLLOP" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fdollop \- Dollo and polymorphism parsimony algorithm .SH "SYNOPSIS" .HP \w'\fBfdollop\fR\ 'u \fBfdollop\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-method\ \fR\fB\fIlist\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfdollop\fR\ 'u \fBfdollop\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfdollop\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIdiscretestates\fR .RS 4 File containing one or more data sets .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 .RE .PP \fB\-ancfile\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-method\fR \fIlist\fR .RS 4 Default value: d .RE .PP \fB\-njumble\fR \fIinteger\fR .RS 4 .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-threshold\fR \fIfloat\fR .RS 4 Default value: $(infile\&.discretesize) .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-ancseq\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-stepbox\fR \fIboolean\fR .RS 4 Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fdollop is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ffactor.1e0000644000000000000000000000573211434420167012645 0ustar '\" t .\" Title: FFACTOR .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FFACTOR" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ffactor \- Multistate to binary recoding program .SH "SYNOPSIS" .HP \w'\fBffactor\fR\ 'u \fBffactor\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR [\fB\-anc\ \fR\fB\fIboolean\fR\fR] [\fB\-factors\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outfactorfile\ \fR\fB\fIoutfile\fR\fR \fB\-outancfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBffactor\fR\ 'u \fBffactor\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBffactor\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Additional section" .PP \fB\-anc\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-factors\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-outfactorfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-outancfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ffactor is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ftreedistpair.1e0000644000000000000000000000625611434420167014070 0ustar '\" t .\" Title: FTREEDISTPAIR .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FTREEDISTPAIR" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ftreedistpair \- Distances between two sets of trees .SH "SYNOPSIS" .HP \w'\fBftreedistpair\fR\ 'u \fBftreedistpair\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR \fB\-bintreefile\ \fR\fB\fItree\fR\fR [\fB\-dtype\ \fR\fB\fIlist\fR\fR] [\fB\-pairing\ \fR\fB\fIlist\fR\fR] [\fB\-style\ \fR\fB\fIlist\fR\fR] [\fB\-noroot\ \fR\fB\fIboolean\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBftreedistpair\fR\ 'u \fBftreedistpair\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBftreedistpair\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Consensus" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .PP \fB\-bintreefile\fR \fItree\fR .RS 4 .RE .SS "Additional section" .PP \fB\-dtype\fR \fIlist\fR .RS 4 Default value: b .RE .PP \fB\-pairing\fR \fIlist\fR .RS 4 Default value: l .RE .PP \fB\-style\fR \fIlist\fR .RS 4 Default value: v .RE .PP \fB\-noroot\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ftreedistpair is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fgendist.1e0000644000000000000000000000554311434420167013024 0ustar '\" t .\" Title: FGENDIST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FGENDIST" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fgendist \- Compute genetic distances from gene frequencies .SH "SYNOPSIS" .HP \w'\fBfgendist\fR\ 'u \fBfgendist\fR \fB\-infile\ \fR\fB\fIfrequencies\fR\fR \fB\-method\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-lower\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfgendist\fR\ 'u \fBfgendist\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfgendist\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Gene frequencies" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIfrequencies\fR .RS 4 File containing one or more sets of data .RE .SS "Additional section" .PP \fB\-method\fR \fIlist\fR .RS 4 Default value: n .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-lower\fR \fIboolean\fR .RS 4 Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fgendist is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/frestboot.1e0000644000000000000000000000753711434420167013235 0ustar '\" t .\" Title: FRESTBOOT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FRESTBOOT" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" frestboot \- Bootstrapped restriction sites algorithm .SH "SYNOPSIS" .HP \w'\fBfrestboot\fR\ 'u \fBfrestboot\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-test\ \fR\fB\fIlist\fR\fR \fB\-regular\ \fR\fB\fItoggle\fR\fR \fB\-fracsample\ \fR\fB\fIfloat\fR\fR \fB\-rewriteformat\ \fR\fB\fIlist\fR\fR \fB\-blocksize\ \fR\fB\fIinteger\fR\fR \fB\-reps\ \fR\fB\fIinteger\fR\fR \fB\-justweights\ \fR\fB\fIlist\fR\fR [\fB\-enzymes\ \fR\fB\fIboolean\fR\fR] \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfrestboot\fR\ 'u \fBfrestboot\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfrestboot\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIdiscretestates\fR .RS 4 File containing one or more sets of restriction data .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 Weights file .RE .SS "Additional section" .PP \fB\-test\fR \fIlist\fR .RS 4 Default value: b .RE .PP \fB\-regular\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-fracsample\fR \fIfloat\fR .RS 4 Default value: 100\&.0 .RE .PP \fB\-rewriteformat\fR \fIlist\fR .RS 4 Default value: p .RE .PP \fB\-blocksize\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-reps\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-justweights\fR \fIlist\fR .RS 4 Default value: d .RE .PP \fB\-enzymes\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-dotdiff\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP frestboot is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fclique.1e0000644000000000000000000000701511434420167012645 0ustar '\" t .\" Title: FCLIQUE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FCLIQUE" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fclique \- Largest clique program .SH "SYNOPSIS" .HP \w'\fBfclique\fR\ 'u \fBfclique\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-factorfile\ \fR\fB\fIproperties\fR\fR] [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-cliqmin\ \fR\fB\fIinteger\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-printcomp\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfclique\fR\ 'u \fBfclique\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfclique\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIdiscretestates\fR .RS 4 .RE .PP \fB\-ancfile\fR \fIproperties\fR .RS 4 .RE .PP \fB\-factorfile\fR \fIproperties\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-cliqmin\fR \fIinteger\fR .RS 4 .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-printcomp\fR \fIboolean\fR .RS 4 Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fclique is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fprotpars.1e0000644000000000000000000001005411434420167013232 0ustar '\" t .\" Title: FPROTPARS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FPROTPARS" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fprotpars \- Protein parsimony algorithm .SH "SYNOPSIS" .HP \w'\fBfprotpars\fR\ 'u \fBfprotpars\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-whichcode\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR .HP \w'\fBfprotpars\fR\ 'u \fBfprotpars\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfprotpars\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqsetall\fR .RS 4 File containing one or more sequence alignments .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-njumble\fR \fIinteger\fR .RS 4 .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .PP \fB\-thresh\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-threshold\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-whichcode\fR \fIlist\fR .RS 4 Default value: Universal .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-stepbox\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-ancseq\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-dotdiff\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fprotpars is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fdnaml.1e0000644000000000000000000001310111434420167012447 0ustar '\" t .\" Title: FDNAML .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FDNAML" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fdnaml \- Estimates nucleotide phylogeny by maximum likelihood .SH "SYNOPSIS" .HP \w'\fBfdnaml\fR\ 'u \fBfdnaml\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-ncategories\ \fR\fB\fIinteger\fR\fR] \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR [\fB\-ttratio\ \fR\fB\fIfloat\fR\fR] [\fB\-freqsfrom\ \fR\fB\fItoggle\fR\fR] \fB\-basefreq\ \fR\fB\fIarray\fR\fR [\fB\-gamma\ \fR\fB\fIlist\fR\fR] \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ngammacat\ \fR\fB\fIinteger\fR\fR \fB\-invarcoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ninvarcat\ \fR\fB\fIinteger\fR\fR \fB\-invarfrac\ \fR\fB\fIfloat\fR\fR \fB\-nhmmcategories\ \fR\fB\fIinteger\fR\fR \fB\-hmmrates\ \fR\fB\fIarray\fR\fR \fB\-hmmprobabilities\ \fR\fB\fIarray\fR\fR \fB\-adjsite\ \fR\fB\fIboolean\fR\fR \fB\-lambda\ \fR\fB\fIfloat\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-rough\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-hypstate\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfdnaml\fR\ 'u \fBfdnaml\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfdnaml\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqsetall\fR .RS 4 File containing one or more sequence alignments .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .PP \fB\-ncategories\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-rate\fR \fIarray\fR .RS 4 .RE .PP \fB\-categories\fR \fIproperties\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 Weights file .RE .SS "Additional section" .PP \fB\-lengths\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-ttratio\fR \fIfloat\fR .RS 4 Default value: 2\&.0 .RE .PP \fB\-freqsfrom\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-basefreq\fR \fIarray\fR .RS 4 Default value: 0\&.25 0\&.25 0\&.25 0\&.25 .RE .PP \fB\-gamma\fR \fIlist\fR .RS 4 Default value: Constant rate .RE .PP \fB\-gammacoefficient\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-ngammacat\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-invarcoefficient\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-ninvarcat\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-invarfrac\fR \fIfloat\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-nhmmcategories\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-hmmrates\fR \fIarray\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-hmmprobabilities\fR \fIarray\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-adjsite\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-lambda\fR \fIfloat\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-njumble\fR \fIinteger\fR .RS 4 .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-global\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .PP \fB\-rough\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-hypstate\fR \fIboolean\fR .RS 4 Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fdnaml is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fpenny.1e0000644000000000000000000001006611434420167012514 0ustar '\" t .\" Title: FPENNY .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FPENNY" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fpenny \- Penny algorithm, branch\-and\-bound .SH "SYNOPSIS" .HP \w'\fBfpenny\fR\ 'u \fBfpenny\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-mixfile\ \fR\fB\fIproperties\fR\fR] \fB\-method\ \fR\fB\fIlist\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-howmany\ \fR\fB\fIinteger\fR\fR] [\fB\-howoften\ \fR\fB\fIinteger\fR\fR] [\fB\-simple\ \fR\fB\fIboolean\fR\fR] [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfpenny\fR\ 'u \fBfpenny\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfpenny\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIdiscretestates\fR .RS 4 File containing one or more data sets .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 .RE .PP \fB\-ancfile\fR \fIproperties\fR .RS 4 .RE .PP \fB\-mixfile\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-method\fR \fIlist\fR .RS 4 Default value: Wagner .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .PP \fB\-howmany\fR \fIinteger\fR .RS 4 Default value: 1000 .RE .PP \fB\-howoften\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-simple\fR \fIboolean\fR .RS 4 .RE .PP \fB\-threshold\fR \fIfloat\fR .RS 4 Default value: $(infile\&.discretesize) .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-stepbox\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-ancseq\fR \fIboolean\fR .RS 4 Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fpenny is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fpars.1e0000644000000000000000000001045311434420167012330 0ustar '\" t .\" Title: FPARS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FPARS" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fpars \- Discrete character parsimony .SH "SYNOPSIS" .HP \w'\fBfpars\fR\ 'u \fBfpars\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-method\ \fR\fB\fIlist\fR\fR [\fB\-maxtrees\ \fR\fB\fIinteger\fR\fR] \fB\-thorough\ \fR\fB\fItoggle\fR\fR \fB\-rearrange\ \fR\fB\fIboolean\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR .HP \w'\fBfpars\fR\ 'u \fBfpars\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfpars\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIdiscretestates\fR .RS 4 File containing one or more data sets .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-method\fR \fIlist\fR .RS 4 Default value: Wagner .RE .PP \fB\-maxtrees\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-thorough\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-rearrange\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-njumble\fR \fIinteger\fR .RS 4 .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .PP \fB\-thresh\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-threshold\fR \fIfloat\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-stepbox\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-ancseq\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-dotdiff\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fpars is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fprotdist.1e0000644000000000000000000000777711434420167013252 0ustar '\" t .\" Title: FPROTDIST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FPROTDIST" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fprotdist \- Protein distance algorithm .SH "SYNOPSIS" .HP \w'\fBfprotdist\fR\ 'u \fBfprotdist\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR [\fB\-ncategories\ \fR\fB\fIinteger\fR\fR] \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-method\ \fR\fB\fIlist\fR\fR \fB\-gamma\ \fR\fB\fIlist\fR\fR \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-invarcoefficient\ \fR\fB\fIfloat\fR\fR \fB\-aacateg\ \fR\fB\fIlist\fR\fR \fB\-whichcode\ \fR\fB\fIlist\fR\fR \fB\-ease\ \fR\fB\fIfloat\fR\fR \fB\-ttratio\ \fR\fB\fIfloat\fR\fR \fB\-basefreq\ \fR\fB\fIarray\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBfprotdist\fR\ 'u \fBfprotdist\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfprotdist\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqsetall\fR .RS 4 File containing one or more sequence alignments .RE .PP \fB\-ncategories\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-rate\fR \fIarray\fR .RS 4 .RE .PP \fB\-categories\fR \fIproperties\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-method\fR \fIlist\fR .RS 4 Default value: j .RE .PP \fB\-gamma\fR \fIlist\fR .RS 4 Default value: c .RE .PP \fB\-gammacoefficient\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-invarcoefficient\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-aacateg\fR \fIlist\fR .RS 4 Default value: G .RE .PP \fB\-whichcode\fR \fIlist\fR .RS 4 Default value: u .RE .PP \fB\-ease\fR \fIfloat\fR .RS 4 Default value: 0\&.457 .RE .PP \fB\-ttratio\fR \fIfloat\fR .RS 4 Default value: 2\&.0 .RE .PP \fB\-basefreq\fR \fIarray\fR .RS 4 Default value: 0\&.25 0\&.25 0\&.25 0\&.25 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fprotdist is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fretree.1e0000644000000000000000000000613111434420167012647 0ustar '\" t .\" Title: FRETREE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FRETREE" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fretree \- Interactive tree rearrangement .SH "SYNOPSIS" .HP \w'\fBfretree\fR\ 'u \fBfretree\fR \fB\-spp\ \fR\fB\fIinteger\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-initialtree\ \fR\fB\fIlist\fR\fR] [\fB\-format\ \fR\fB\fIlist\fR\fR] [\fB\-screenwidth\ \fR\fB\fIinteger\fR\fR] [\fB\-vscreenwidth\ \fR\fB\fIinteger\fR\fR] [\fB\-screenlines\ \fR\fB\fIinteger\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBfretree\fR\ 'u \fBfretree\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfretree\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Tree drawing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-spp\fR \fIinteger\fR .RS 4 .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .SS "Additional section" .PP \fB\-initialtree\fR \fIlist\fR .RS 4 Default value: Arbitary .RE .PP \fB\-format\fR \fIlist\fR .RS 4 Default value: p .RE .PP \fB\-screenwidth\fR \fIinteger\fR .RS 4 Default value: 80 .RE .PP \fB\-vscreenwidth\fR \fIinteger\fR .RS 4 Default value: 80 .RE .PP \fB\-screenlines\fR \fIinteger\fR .RS 4 Default value: 24 .RE .SS "Output section" .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fretree is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fmove.1e0000644000000000000000000000700111434420167012324 0ustar '\" t .\" Title: FMOVE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FMOVE" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fmove \- Interactive mixed method parsimony .SH "SYNOPSIS" .HP \w'\fBfmove\fR\ 'u \fBfmove\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-factorfile\ \fR\fB\fIproperties\fR\fR] \fB\-method\ \fR\fB\fIlist\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] [\fB\-initialtree\ \fR\fB\fIlist\fR\fR] [\fB\-screenwidth\ \fR\fB\fIinteger\fR\fR] [\fB\-screenlines\ \fR\fB\fIinteger\fR\fR] [\fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBfmove\fR\ 'u \fBfmove\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfmove\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIdiscretestates\fR .RS 4 File containing data set .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 Weights file .RE .PP \fB\-ancfile\fR \fIproperties\fR .RS 4 .RE .PP \fB\-factorfile\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-method\fR \fIlist\fR .RS 4 Default value: Wagner .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .PP \fB\-threshold\fR \fIfloat\fR .RS 4 Default value: $(infile\&.discretesize) .RE .PP \fB\-initialtree\fR \fIlist\fR .RS 4 Default value: Arbitary .RE .PP \fB\-screenwidth\fR \fIinteger\fR .RS 4 Default value: 80 .RE .PP \fB\-screenlines\fR \fIinteger\fR .RS 4 Default value: 24 .RE .SS "Output section" .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fmove is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fdrawgram.1e0000644000000000000000000001151011434420167013162 0ustar '\" t .\" Title: FDRAWGRAM .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FDRAWGRAM" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fdrawgram \- Plots a cladogram\- or phenogram\-like rooted tree diagram .SH "SYNOPSIS" .HP \w'\fBfdrawgram\fR\ 'u \fBfdrawgram\fR \fB\-fontfile\ \fR\fB\fIstring\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR \fB\-plotfile\ \fR\fB\fIoutfile\fR\fR [\fB\-grows\ \fR\fB\fIboolean\fR\fR] [\fB\-style\ \fR\fB\fIlist\fR\fR] [\fB\-plotter\ \fR\fB\fIlist\fR\fR] [\fB\-previewer\ \fR\fB\fIlist\fR\fR] [\fB\-lengths\ \fR\fB\fIboolean\fR\fR] \fB\-labelrotation\ \fR\fB\fIfloat\fR\fR [\fB\-rescaled\ \fR\fB\fItoggle\fR\fR] \fB\-bscale\ \fR\fB\fIfloat\fR\fR [\fB\-treedepth\ \fR\fB\fIfloat\fR\fR] [\fB\-stemlength\ \fR\fB\fIfloat\fR\fR] [\fB\-nodespace\ \fR\fB\fIfloat\fR\fR] [\fB\-nodeposition\ \fR\fB\fIlist\fR\fR] \fB\-xmargin\ \fR\fB\fIfloat\fR\fR \fB\-ymargin\ \fR\fB\fIfloat\fR\fR \fB\-xrayshade\ \fR\fB\fIfloat\fR\fR \fB\-yrayshade\ \fR\fB\fIfloat\fR\fR [\fB\-paperx\ \fR\fB\fIfloat\fR\fR] [\fB\-papery\ \fR\fB\fIfloat\fR\fR] [\fB\-pagesheight\ \fR\fB\fIfloat\fR\fR] [\fB\-pageswidth\ \fR\fB\fIfloat\fR\fR] [\fB\-hpmargin\ \fR\fB\fIfloat\fR\fR] [\fB\-vpmargin\ \fR\fB\fIfloat\fR\fR] .HP \w'\fBfdrawgram\fR\ 'u \fBfdrawgram\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfdrawgram\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Tree drawing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-fontfile\fR \fIstring\fR .RS 4 Default value: font1 .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .SS "Additional section" .SS "Output section" .PP \fB\-plotfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-grows\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-style\fR \fIlist\fR .RS 4 Default value: c .RE .PP \fB\-plotter\fR \fIlist\fR .RS 4 Default value: l .RE .PP \fB\-previewer\fR \fIlist\fR .RS 4 Default value: x .RE .PP \fB\-lengths\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-labelrotation\fR \fIfloat\fR .RS 4 Default value: 90\&.0 .RE .PP \fB\-rescaled\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-bscale\fR \fIfloat\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-treedepth\fR \fIfloat\fR .RS 4 Default value: 0\&.53 .RE .PP \fB\-stemlength\fR \fIfloat\fR .RS 4 Default value: 0\&.05 .RE .PP \fB\-nodespace\fR \fIfloat\fR .RS 4 Default value: 0\&.3333 .RE .PP \fB\-nodeposition\fR \fIlist\fR .RS 4 Default value: c .RE .PP \fB\-xmargin\fR \fIfloat\fR .RS 4 Default value: 1\&.65 .RE .PP \fB\-ymargin\fR \fIfloat\fR .RS 4 Default value: 2\&.16 .RE .PP \fB\-xrayshade\fR \fIfloat\fR .RS 4 Default value: 1\&.65 .RE .PP \fB\-yrayshade\fR \fIfloat\fR .RS 4 Default value: 2\&.16 .RE .PP \fB\-paperx\fR \fIfloat\fR .RS 4 Default value: 20\&.63750 .RE .PP \fB\-papery\fR \fIfloat\fR .RS 4 Default value: 26\&.98750 .RE .PP \fB\-pagesheight\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-pageswidth\fR \fIfloat\fR .RS 4 Default value: 1 .RE .PP \fB\-hpmargin\fR \fIfloat\fR .RS 4 Default value: 0\&.41275 .RE .PP \fB\-vpmargin\fR \fIfloat\fR .RS 4 Default value: 0\&.53975 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fdrawgram is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fdnapars.1e0000644000000000000000000001053111434420167013010 0ustar '\" t .\" Title: FDNAPARS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: PHYLIPNEW 3.69+20100721 .\" Language: English .\" .TH "FDNAPARS" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fdnapars \- DNA parsimony algorithm .SH "SYNOPSIS" .HP \w'\fBfdnapars\fR\ 'u \fBfdnapars\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-maxtrees\ \fR\fB\fIinteger\fR\fR] \fB\-thorough\ \fR\fB\fItoggle\fR\fR \fB\-rearrange\ \fR\fB\fIboolean\fR\fR [\fB\-transversion\ \fR\fB\fIboolean\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR .HP \w'\fBfdnapars\fR\ 'u \fBfdnapars\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfdnapars\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqsetall\fR .RS 4 File containing one or more sequence alignments .RE .PP \fB\-intreefile\fR \fItree\fR .RS 4 .RE .PP \fB\-weights\fR \fIproperties\fR .RS 4 .RE .SS "Additional section" .PP \fB\-maxtrees\fR \fIinteger\fR .RS 4 Default value: 10000 .RE .PP \fB\-thorough\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-rearrange\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-transversion\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-njumble\fR \fIinteger\fR .RS 4 .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-outgrno\fR \fIinteger\fR .RS 4 .RE .PP \fB\-thresh\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-threshold\fR \fIfloat\fR .RS 4 Default value: 1\&.0 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-trout\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outtreefile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-printdata\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-progress\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-stepbox\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-ancseq\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-treeprint\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-dotdiff\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fdnapars is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/changelog0000644000000000000000000000574712216642047011061 0ustar embassy-phylip (3.69.650-2) unstable; urgency=low * Fixed versioned Depends Closes: #723735 -- Andreas Tille Thu, 19 Sep 2013 20:35:31 +0200 embassy-phylip (3.69.650-1) unstable; urgency=low * New upstream version * debian/control: - cme fix dpkg-control - Bumped versioned depends from emboss-lib - anonscm in VCS fields - added XS-Autobuild: yes -- Andreas Tille Thu, 12 Sep 2013 10:32:23 +0200 embassy-phylip (3.69+20110714-1) unstable; urgency=low * New upstream version * debian/control: - Standards-Version: 3.9.3 (no changes needed) - debhelper version 9 - Adapted versioned (build-)depends to latest emboss version * debian/compat: 9 * debian/source/format: 3.0 (quilt) * debian/rules: short dh * debian/embassy-phylip.lintian-overrides: Handle false positive when detecting the string "GPL" inside debian/copyright -- Andreas Tille Wed, 04 Jul 2012 14:54:50 +0200 embassy-phylip (3.69+20100721-3) unstable; urgency=low * Set RPATH with “-Wl,--rpath” as GCC 4.6 does not accept “-R” anymore. (debian/rules) LP: #770835. * Incremented Standards-Version to reflect conformance with Policy 3.9.2 (debian/control, no changes needed). * Updated debian/embassy-phylip.lintian-overrides for lintian 2.5. * debian/copyright validated with config-edit. -- Charles Plessy Thu, 12 May 2011 14:19:59 +0900 embassy-phylip (3.69+20100721-2) unstable; urgency=low * Built on emboss-lib 6.3.1-6, pre-emptively depending on versions lower than 6.3.2, because backwards compatibility is sometimes broken (debian/control, debian/rules). * Set an RPATH to /usr/lib/emboss/lib for using EMBOSS private libraries (debian/rules, debian/embassy-phylip.lintian-overrides). * Refreshed debian/copyright to test the latest DEP-5 format. -- Charles Plessy Thu, 23 Sep 2010 14:07:26 +0900 embassy-phylip (3.69+20100721-1) unstable; urgency=low * New upstream release in which the version number was unchanged. * Build-Depends on emboss 6.3.1 (debian/control, debian/rules). * Build-Depends on libmysqlclient-dev and libpq-dev until emboss is fixed. * Pass -Wl,--as-needed to avoid unneeded binary dependencies (debian/rules). * Incremented Standards-Version to reflect conformance with Policy 3.9.1 (debian/control, no changes needed). -- Charles Plessy Wed, 11 Aug 2010 19:46:37 +0900 embassy-phylip (3.69-1) unstable; urgency=low * New upstream release. * debian/control: - Corrected Vcs-Browser URL. - Incremented Standards-Version to reflect conformance with Policy 3.8.4 (no changes needed). * Refreshed the manual pages (Debian-specific). -- Charles Plessy Tue, 01 Jun 2010 21:43:33 +0900 embassy-phylip (3.68-1) unstable; urgency=low * Initial release (Closes: #493977) -- Charles Plessy Sat, 08 Aug 2009 16:59:11 +0900 debian/source/0000755000000000000000000000000012214275755010500 5ustar debian/source/format0000644000000000000000000000001411507156767011713 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000211775036547010403 0ustar 9 debian/rules0000755000000000000000000000043511771050574010257 0ustar #!/usr/bin/make -f CFLAGS += -I/usr/lib/emboss/include -I/usr/lib/emboss/include/epcre -I/usr/lib/emboss/include/eplplot -L/usr/lib/emboss/lib -Wl,--rpath,/usr/lib/emboss/lib LDFLAGS += -Wl,--as-needed %: dh $@ override_dh_auto_configure: dh_auto_configure -- --enable-systemlibs debian/embassy-phylip.lintian-overrides0000644000000000000000000000063411775043431015524 0ustar # The embassy packages use privately some of the EMBOSS libraries. They have # the same upstream authors and are released together. embassy-phylip: binary-or-shlib-defines-rpath * # debian/copyright actually states that the code is *not* GPL in contrast # to what the upstream COPYRIGHT file says. So this is a false positive # from lintian embassy-phylip: copyright-should-refer-to-common-license-file-for-gpl debian/control0000644000000000000000000000351112216641755010602 0ustar Source: embassy-phylip Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: non-free/science Priority: optional Build-Depends: debhelper (>= 9), autotools-dev, libxaw7-dev, emboss-lib (>= 6.6.0-1~), emboss-lib (<< 6.6.1~), libgd2-xpm-dev, libmysqlclient-dev, libpq-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/embassy-phylip/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/embassy-phylip/trunk/ Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#PHYLIPNEW XS-Autobuild: yes Package: embassy-phylip Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, emboss-lib (>= 6.6.0-1~), emboss-lib (<< 6.6.1~) Description: EMBOSS conversions of the programs in the phylip package This package is the adaptation of the PHYLIP package in which its programs can operate with the biological sequence formats and databases of the European Molecular Biology Open Software Suite (EMBOSS). The software packages adapted for EMBOSS are called EMBASSY. . PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters. . The EMBASSY PHYLIP programs all have the prefix "f" to distinguish them from the original programs and avoid namespace conflict. debian/embassy-phylip.manpages0000644000000000000000000000213411434420167013653 0ustar debian/manpages/fclique.1e debian/manpages/fconsense.1e debian/manpages/fcontml.1e debian/manpages/fcontrast.1e debian/manpages/fdiscboot.1e debian/manpages/fdnacomp.1e debian/manpages/fdnadist.1e debian/manpages/fdnainvar.1e debian/manpages/fdnaml.1e debian/manpages/fdnamlk.1e debian/manpages/fdnamove.1e debian/manpages/fdnapars.1e debian/manpages/fdnapenny.1e debian/manpages/fdollop.1e debian/manpages/fdolmove.1e debian/manpages/fdolpenny.1e debian/manpages/fdrawgram.1e debian/manpages/fdrawtree.1e debian/manpages/ffactor.1e debian/manpages/ffitch.1e debian/manpages/ffreqboot.1e debian/manpages/fgendist.1e debian/manpages/fkitsch.1e debian/manpages/fmix.1e debian/manpages/fmove.1e debian/manpages/fneighbor.1e debian/manpages/fpars.1e debian/manpages/fpenny.1e debian/manpages/fproml.1e debian/manpages/fpromlk.1e debian/manpages/fprotdist.1e debian/manpages/fprotpars.1e debian/manpages/frestboot.1e debian/manpages/frestdist.1e debian/manpages/frestml.1e debian/manpages/fretree.1e debian/manpages/fseqboot.1e debian/manpages/fseqbootall.1e debian/manpages/ftreedist.1e debian/manpages/ftreedistpair.1e debian/docs0000644000000000000000000000002111237220540010026 0ustar ChangeLog README