debian/0000755000000000000000000000000012202264422007162 5ustar debian/menu0000644000000000000000000000040111110210632010033 0ustar ?package(seaview):\ needs="X11"\ section="Applications/Science/Biology"\ hints="Multiple sequence alignment"\ longtitle="SeaView: multiple sequence alignment editor"\ title="SeaView"\ command="/usr/bin/seaview"\ icon="/usr/share/pixmaps/seaview.xpm" debian/example_files/0000755000000000000000000000000012201733374012005 5ustar debian/example_files/nuc.aln0000644000000000000000000000372211725503373013276 0ustar CLUSTAL W (1.7) multiple sequence alignment seq4 ----------------------------NNNNATACTCTG-GTTTCTCTTCAGATCGTAT seq6 ----------------------------NNNNATACTCTG-GTTTCTCTTCAGATCGCAT seq5 ------------------------------------------------------------ seq2 TATGCAGACAATTATGATTACATGGGGTAAAAATACTCCAAGATAGTATTCAGTTCTCAA seq1 ------AAGCTTTATTTTTCCATCTCTTTTACAT--TCAATGATTCTATTCATTTGT-AA seq3 ------------------------------------------------------------ seq4 AAATCTTTCCCCTTTCANCAAAGATTTCCGTGGAGAGGAATAACTCTGAGTC--TTAAGC seq6 AAATCTTTCCCCTTTCANCAAAGATTTCCGTGGAGAGGAACAACTCTGAGTC--TTAACC seq5 ------------------------------------------------------------ seq2 GATGGTTCATCACATTTGCCAAGTTTTTCTACCATAAAATTCCCCACCAATCCATTTATG seq1 GAGAAGTAAGCANNNNNNACTCCAACAGTGGAGAAAGTCAGACTGATTAAACAGGTNNAC seq3 -----------------------GTCTACGGCCATACCACCCTGAACGCGCCCGATCTCG seq4 TAATTTTTTGAGCCTT------GCTCCGACAAGGCTA----------------------- seq6 CAATTTTTTGAGCCTT------GCCTTGGCAAGGCTA----------------------- seq5 ----------AGCCTT------GTTCCGACAAGGCTA----------------------- seq2 TATAGAGTTGATAGTTAACAGAGATCGGAAATGGCCATTGCATCTTTAGTCTGGATTTCC seq1 CAAACACGTAAATGTTTTT--GNAGAAGGAAGGGNAACTCTGGTGAGCCCGCAGAGGTGC seq3 TCTGATCTCGGAAGCTAAGCAGGGTCGGGCCTGGTTAGTACTTGGATGG--GAGACCGCC * * ** * seq4 ------------------------------- seq6 ------------------------------- seq5 ------------------------------- seq2 TGAGACCTTTGGTTTATTTCTAGGGCTGC-- seq1 ACAGGCTNNNTAGAGACAGCAGTGTCAGTCC seq3 TGGGAATACCGGGTGCTGTAGGCTTT----- debian/example_files/seq.fas0000644000000000000000000001603211725503374013277 0ustar >gi|2981175 deltex MSRPGHGGLMPVNGLGFPPQNVARVVVWECLNEHSRWRPYTATVCHHIENVLKEDARGSVVLGQVDAQLV PYIIDLQSMHQFRQDTGTMRPVRRNFYDPSSAPGKGIVWEWENDGGAWTAYDMDICITIQNAYEKQHPWL DLSSLGFCYLIYFNSMSQMNRQTRRRRRLRRRLDLAYPLTVGSIPKSQSWPVGASSGQPCSCQQCLLVNS TRAVSNVILASQRRKVPPAPPLPPPPPPGGPPGALAVRPSATFTGAALWAAPAAGPAEPAPPPGAPPRSP GAPGGARTPGQNNLNRPGPQRTTSVSARASIPPGVPALPVKNLNGTGPVHPALAGMTGILLCAAGLPVCL TRAPKPILHPPPVSKSDVKPVPGVPGVCRKTKKKHLKKSKNPEDVVRRYMQKVKNPPDEDCTICMERLVT ASGYEGVLRHKGVRPELVGRLGRCGHMYHLLCLVAMYSNGNKDGSLQCPTCKAIYGEKTGTQPPGKMEFH LIPHSLPGFPDTQTIRIVYDIPTGIQGPEHPNPGKKFTARGFPRHCYLPNNEKGRKVLRLLITAWERRLI FTIGTSNTTGESDTVVWNEIHHKTEFGSNLTGHGYPDASYLDNVLAELTAQGVSEAAGKAU >gi|927067 longation factor 1-alpha 1 MQSERGITIDISLWKFETSKYYVTIIDAPGHRDFIQNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTR EHALLAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEP SANMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLGLPLQDVYKIGGIGTVPVGRVETGVLKP GMVVTFGPVNVTTEVKSVEMHHEALGEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFPAQV IILNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVES FSDYPPLGCFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK >gi|927065 elongation factor 1-alpha 1 MQSERGITIDISLWKFETSKYYVTIIDAPGHRDFIQNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTR EHALLAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEP SANMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLGLPLQDVYKIGGIGTVPVGRVETGVLKP GMVVTFGPVNVTTEVKSVEMHHEALGEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFPAQV IILNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVES FSDYPPLGCFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK >gi|2981019 transcription factor POU4F3 MMAMNSKQPFGMHPVLQEPKFSSLHSGSEAMRRVCLPAPQLQGNIFGSFDESLLARAEALAAVDIVFHGK NHPFKPDATYHTMSSVPCTSTSSTVPISHPAALTSHPHHAVHQGLEGDLLEHISPTLSVSGLGAPEHSVM PAQIHPHHLGAMGHLHQAMGMSHPHTVAPHSAMPACLSDVESDPRELEAFAERFKQRRIKLGVTQADVGA ALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPVLQAWLEEAEAAYREKNSKPELFNGSERKRKRTS IAAPEKRSLEAYFAIQPRPSSEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKYSAVH >gi|2980872|gnl|PID|e1283615 homeobox protein SHOTb MEDEGQTKIKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQVWFQNRRAKCRKQE NQLHKGVLIGAASQFEACRVAPYVNVGALRMPFQQVQAQLQLDSAVAHAHHHLHPHLAAHAPYMMFPAPP FGLPLATLAADSASAASVVAAAAAAKTTSKDSSIADLRLKAKKHAAALGL >gi|2980870|gnl|PID|e1283613 homeobox protein SHOTa GGAGGGAGGGRSPVRELDMGAAERSREPGSPRLTEVSPELKDRKEDAKGMEDEGQTKIKQRRSRTNFTLE QLNELERLFDETHYPDAFMREELSQRLGLSEARVQVWFQNRRAKCRKQENQLHKGVLIGAASQFEACRVA PYVNVGALRMPFQQDSHCNVTPLPFQVQAQLQLDSAVAHAHHHLHPHLAAHAPYMMFPAPPFGLPLATLA ADSASAASVVAAAAAAKTTSKDSSIADLRLKAKKHAAALGL >gi|2980865|gnl|PID|e1283649 NKG2D MGWIRGRRSRHSWEMSEFHNYNLDLKKSDFSTRWQKQRCPVVKSKCRENASPFFFCCFIAVAMGIRFIIM VAIWSAVFLNSLFNQEVQIPLTESYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKVYSK EDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLTIIEMQKGDCALYASSFKGYIENCSTPNTYI CMQRTV >gi|2980863|gnl|PID|e1283645 NKG2F MNKQRGTYSEVSLAQDPKRQQRKLKGNKSSISGTKQEIFQVELNLQNASSDHQGNDKTYHCKGLLPPPEK LTAEVLGIICIVLMATVLKTIVLIPCIGVLEQNSFSLNRRMQKARHCGHCPEEWITYSNSCYYIGKERRT WEERVCWPVLRRTLICFL >gi|2980861|gnl|PID|e1283610 NKG2E MNKQRGTFSEVSLAQDPKPQQRKPKGNKSSISGTEQEIFQVELNLQNASLNHQGIDKIYDCQGLLPPPEK LTAEVLGIICIVLMATVLKTIVLIPFLEQNNSSPNTRTQKARPCGHCPEEWITYSNSCYYIGKERRTWEE SLQACASKNSSSLLSIDNEEEMKFLASILPSSWIGVFRNSSHHPWVTINGLAFKHEIKDSDHAERNCAML HVRGLISDQCGSSRIIRRGFIMLTRLVLNS >gi|2980859|gnl|PID|e1283608 NKG2C MSKQRGTFSEVSLAQDPKRQQRKPKGNKSSISGTEQEIFQVELNLQNPSLNHQGIDKIYDCQGLLPPPEK LTAEVLGIICIVLMATVLKTIVLIPFLEQNNSSPNTRTQKARHCGHCPEEWITYSNSCYYIGKERRTWEE SLLACTSKNSSLLSIDNEEEMKFLASILPSSWIGVFRNSSHHPWVTINGLAFKHKIKDSDNAELNCAVLQ VNRLKSAQCGSSMIYHCKHKL >gi|2980857|gnl|PID|e1283606 NKG2F MNKQRGTYSEVSLAQDPKRQQRKLKGNKISISGTKQEIFQVELNLQNASSDHQGNDKTYHCKGLLPPPEK LTAEVLGIICIVLMATVLKTIVLIPCIGVLEQNNFSLNRRMQKARHCGHCPEEWITYSNSCYYIGKERRT WEERVCWPVLRRTLICFL >gi|2979422|gnl|PID|d1026124 PCDH7 (BH-Pcdh)c MLRMRTAGWARGWCLGCCLLLPLSFSLAAAKQLLRYRLAEEGPADVRIGNVASDLGIVTGSGEVTFSLES GSEYLKIDNLTGELSTSERRIDREKLPQCQMIFDENECFLDFEVSVIGPSQSWVDLFEGQVIVLDINDNT PTFPSPVLTLTVEENRPVGTLYLLPTATDRDFGRNGIERYELLQEPGGGGSGGESRRAGAADSAPYPGGG GNGASGGGSGGSKRRLDASEGGGGTNPGGRSSVFELQVADTPDGEKQPQLIVKGVYEADLAENSAPGTPI LQLRAADLDVGVNGQIEYVFGAATESVRRLLRLDETSGWLSVLHRIDREEVNQLRFTVMARDRGQPPKTD KATVVLNIKDENDNVPSIEIRKIGRIPLKDGVANVAEDVLVDTPIALVQVSDRDQGENGVVTCTVVGDVP FQLKPASDTEGDQNKKKYFLHTSTPLDYEATREFNVVIVAVDSGSPSLSSKNSLIVKVGDTNDNPPMFGQ SVVEVYFPENNIPGERVATVLATDADSGKNAEIAYSLDSSVMGIFAIDPDSGDILVNTVLDREQTDRYEF KVNAKDKGIPVLQGSTTVIVQVADKNDNDPKFMQDVFTFYVKENLQPNSPVGMVTVMDADKGRNAEMSLY IEENNNIFSIENDTGTIYSTMSFDREHQTTYTFRVKAVDGGDPPRSATATVSLFVMDENDNAPTVTLPKN ISYTLLPPSSNVRTVVATVLATDSDDGINADLNYSIVGGNPFKLFEIDPTSGVVSLVGKLTQKHYGLHRL VVQVNDSGQPSQSTTTVVHVFVNESVSNATAIDSQIARSLHIPLTQDIAGDPSYEISKQRLSIVIGVVAG IMTVILIILIVVMARYCRSKNKNGYEAGKKDHEDFFTPQQHDKSKKPKKDKKNKKSKQPLYSSIVTVEAS KPNGQRYDSVNEKLSDSPSMGRYRSVNGGPGSPDLARHYKSSSPLPTVQLHPQSPTAGKKHQAVQDLPPA NTFVGAGDNISIGSDHCSEYSCQTNNKYSKQPFRRVTFSVVSQPQDPHQGSLQSCYDSGLEESETPSSKS SSGPRLGALPLPEDNYERTTPDGSVDSRPLPDVALTGKCTRECDEYGHSDSCWMPVRTSPERKKSQPKLS TFMPVDERGSQEKLANGEAAIMGDRNRNLLNKKLTSSYETFSAASFSKNEEANPEDIPLTKTGEYKPSPV NTLTRREVYL >gi|2979420|gnl|PID|d1026123 PCDH7 (BH-Pcdh)b MLRMRTAGWARGWCLGCCLLLPLSFSLAAAKQLLRYRLAEEGPADVRIGNVASDLGIVTGSGEVTFSLES GSEYLKIDNLTGELSTSERRIDREKLPQCQMIFDENECFLDFEVSVIGPSQSWVDLFEGQVIVLDINDNT PTFPSPVLTLTVEENRPVGTLYLLPTATDRDFGRNGIERYELLQEPGGGGSGGESRRAGAADSAPYPGGG GNGASGGGSGGSKRRLDASEGGGGTNPGGRSSVFELQVADTPDGEKQPQLIVKGALDREQRDSYELTLRV RDGGDPPRSSQAILRVLITDVNDNSPRFEKSVYEADLAENSAPGTPILQLRAADLDVGVNGQIEYVFGAA TESVRRLLRLDETSGWLSVLHRIDREEVNQLRFTVMARDRGQPPKTDKATVVLNIKDENDNVPSIEIRKI GRIPLKDGVANVAEDVLVDTPIALVQVSDRDQGENGVVTCTVVGDVPFQLKPASDTEGDQNKKKYFLHTS TPLDYEATREFNVVIVAVDSGSPSLSSKNSLIVKVGDTNDNPPMFGQSVVEVYFPENNIPGERVATVLAT DADSGKNAEIAYSLDSSVMGIFAIDPDSGDILVNTVLDREQTDRYEFKVNAKDKGIPVLQGSTTVIVQVA DKNDNDPKFMQDVFTFYVKENLQPNSPVGMVTVMDADKGRNAEMSLYIEENNNIFSIENDTGTIYSTMSF DREHQTTYTFRVKAVDGGDPPRSATATVSLFVMDENDNAPTVTLPKNISYTLLPPSSNVRTVVATVLATD SDDGINADLNYSIVGGNPFKLFEIDPTSGVVSLVGKLTQKHYGLHRLVVQVNDSGQPSQSTTTVVHVFVN ESVSNATAIDSQIARSLHIPLTQDIAGDPSYEISKQRLSIVIGVVAGIMTVILIILIVVMARYCRSKNKN GYEAGKKDHEDFFTPQQHDKSKKPKKDKKNKKSKQPLYSSIVTVEASKPNGQRYDSVNEKLSDSPSMGRY RSVNGGPGSPDLARHYKSSSPLPTVQLHPQSPTAGKKHQAVQDLPPANTFVGAGDNISIGSDHCSEYSCQ TNNKYSKQVRCIPNIFKYPREG >gi|2979418|gnl|PID|d1026122 PCDH7 (BH-Pcdh)a MLRMRTAGWARGWCLGCCLLLPLSFSLAAAKQLLRYRLAEEGPADVRIGNVASDLGIVTGSGEVTFSLES GSEYLKIDNLTGELSTSERRIDREKLPQCQMIFDENECFLDFEVSVIGPSQSWVDLFEGQVIVLDINDNT PTFPSPVLTLTVEENRPVGTLYLLPTATDRDFGRNGIERYELLQEPGGGGSGGESRRAGAADSAPYPGGG GNGASGGGSGGSKRRLDASEGGGGTNPGGRSSVFELQVADTPDGEKQPQLIVKGALDREQRDSYELTLRV RDGGDPPRSSQAILRVLITDVNDNSPRFEKSVYEADLAENSAPGTPILQLRAADLDVGVNGQIEYVFGAA TESVRRLLRLDETSGWLSVLHRIDREEVNQLRFTVMARDRGQPPKTDKATVVLNIKDENDNVPSIEIRKI GRIPLKDGVANVAEDVLVDTPIALVQVSDRDQGENGVVTCTVVGDVPFQLKPASDTEGDQNKKKYFLHTS TPLDYEATREFNVVIVAVDSGSPSLSSKNSLIVKVGDTNDNPPMFGQSVVEVYFPENNIPGERVATVLAT DADSGKNAEIAYSLDSSVMGIFAIDPDSGDILVNTVLDREQTDRYEFKVNAKDKGIPVLQGSTTVIVQVA DKNDNDPKFMQDVFTFYVKENLQPNSPVGMVTVMDADKGRNAEMSLYIEENNNIFSIENDTGTIYSTMSF DREHQTTYTFRVKAVDGGDPPRSATATVSLFVMDENDNAPTVTLPKNISYTLLPPSSNVRTVVATVLATD SDDGINADLNYSIVGGNPFKLFEIDPTSGVVSLVGKLTQKHYGLHRLVVQVNDSGQPSQSTTTVVHVFVN ESVSNATAIDSQIARSLHIPLTQDIAGDPSYEISKQRLSIVIGVVAGIMTVILIILIVVMARYCRSKNKN GYEAGKKDHEDFFTPQQHDKSKKPKKDKKNKKSKQPLYSSIVTVEASKPNGQRYDSVNEKLSDSPSMGRY RSVNGGPGSPDLARHYKSSSPLPTVQLHPQSPTAGKKHQAVQDLPPANTFVGAGDNISIGSDHCSEYSCQ TNNKYSKQMRLHPYITVFG debian/example_files/dna.phy0000644000000000000000000000404611725503374013302 0ustar 7 232 Bovine CCAAACCTGT CCCCACCATC TAACACCAAC CCACATATAC AAGCTAAACC AAAAATACCA Mouse CCAAAAAAAC ATCCAAACAC CAACCCCAGC CCTTACGCAA TAGCCATACA AAGAATATTA Gibbon CTATACCCAC CCAACTCGAC CTACACCAAT CCCCACATAG CACACAGACC AACAACCTCC Orang CCCCACCCGT CTACACCAGC CAACACCAAC CCCCACCTAC TATACCAACC AATAACCTCT Gorilla CCCCATTTAT CCATAAAAAC CAACACCAAC CCCCATCTAA CACACAAACT AATGACCCCC Chimp CCCCATCCAC CCATACAAAC CAACATTACC CTCCATCCAA TATACAAACT AACAACCTCC Human CCCCACTCAC CCATACAAAC CAACACCACT CTCCACCTAA TATACAAATT AATAACCTCC TACTACTAAA AACTCAAATT AACTCTTTAA TCTTTATACA ACATTCCACC AACCTATCCA TACAACCATA AATAAGACTA ATCTATTAAA ATAACCCATT ACGATACAAA ATCCCTTTCG CACCTTCCAT ACCAAGCCCC GACTTTACCG CCAACGCACC TCATCAAAAC ATACCTACAA CAACCCCTAA ACCAAACACT ATCCCCAAAA CCAACACACT CTACCAAAAT ACACCCCCAA CACCCTCAAA GCCAAACACC AACCCTATAA TCAATACGCC TTATCAAAAC ACACCCCCAA CACTCTTCAG ACCGAACACC AATCTCACAA CCAACACGCC CCGTCAAAAC ACCCCTTCAG CACCTTCAGA ACTGAACGCC AATCTCATAA CCAACACACC CCATCAAAGC ACCCCTCCAA CACAAAAAAA CTCATATTTA TCTAAATACG AACTTCACAC AACCTTAACA CATAAACATA TCTAGATACA AACCACAACA CACAATTAAT ACACACCACA ATTACAATAC TAAACTCCCA CACAAACAAA TGCCCCCCCA CCCTCCTTCT TCAAGCCCAC TAGACCATCC TACCTTCCTA TTCACATCCG CACACCCCCA CCCCCCCTGC CCACGTCCAT CCCATCACCC TCTCCTCCCA CATAAACCCA CGCACCCCCA CCCCTTCCGC CCATGCTCAC CACATCATCT CTCCCCTTCA CACAAATTCA TACACCCCTA CCTTTCCTAC CCACGTTCAC CACATCATCC CCCCCTCTCA CACAAACCCG CACACCTCCA CCCCCCTCGT CTACGCTTAC CACGTCATCC CTCCCTCTCA CCCCAGCCCA ACACCCTTCC ACAAATCCTT AATATACGCA CCATAAATAA CA TCCCACCAAA TCACCCTCCA TCAAATCCAC AAATTACACA ACCATTAACC CA GCACGCCAAG CTCTCTACCA TCAAACGCAC AACTTACACA TACAGAACCA CA ACACCCTAAG CCACCTTCCT CAAAATCCAA AACCCACACA ACCGAAACAA CA ACACCTCAAT CCACCTCCCC CCAAATACAC AATTCACACA AACAATACCA CA ACATCTTGAC TCGCCTCTCT CCAAACACAC AATTCACGCA AACAACGCCA CA ACACCTTAAC TCACCTTCTC CCAAACGCAC AATTCGCACA CACAACGCCA CA debian/manpages0000644000000000000000000000001211224705076010701 0ustar seaview.1 debian/source/0000755000000000000000000000000012201733374010470 5ustar debian/source/format0000644000000000000000000000001411301174376011677 0ustar 3.0 (quilt) debian/docs0000644000000000000000000000003711204030730010027 0ustar seaview.html debian/references debian/install0000644000000000000000000000027011702646747010574 0ustar seaview usr/bin seaview.xpm usr/share/pixmaps seaview.html usr/share/seaview debian/seaview.desktop usr/share/applications debian/seaview.svg usr/share/icons/hicolor/scalable/apps debian/dirs0000644000000000000000000000005311110210632010033 0ustar /usr/share/pixmaps /usr/share/applications debian/copyright0000644000000000000000000001535512033761366011141 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.4.0.tar.gz Disclamer: This package is not part of the Debian operating system. The seaview source and binary Debian packages are part of the “non-free” area in our 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 licences of SeaView do not forbid Debian from using autobuilders to create binary packages. Files: * Copyright: 1996-2010 Manolo Gouy License: GPL-3+ with PHYLIP exception This program, except where indicated, is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.. . Two files (dnapars.c and protpars.c) have a distinct license which authorizes distribution that does not generate revenue. . Three files (bionj.c, phyml_util.c and phyml_util.h) are also covered by the GNU General Public License but are copyright Stephane Guindon. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . Additional permission under GNU GPL version 3 section 7 . If you modify this Program, or any covered work, by linking or combining it with PHYLIP (or a modified version of that library), containing parts covered by the terms of the University of Washington license, the licensor of this Program grants you additional permission to convey the resulting work. . A copy of the GNU General Public License is available from http://www.gnu.org/licenses/gpl.txt . Comment: On Debian systems, the complete text of the GNU General Public License version 3 can be found in ‘/usr/share/common-licenses/GPL-3’. Files: csrc/bionj.c csrc/phyml_util.h Copyright: © Stephane Guindon. Oct 2003 onward License: GPL-2+ with PHYLIP exception This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program; if not, see . . Linking PHYML statically or dynamically with other modules is making a combined work based on PHYML. Thus, the terms and conditions of the GNU General Public License cover the whole combination. . In addition, as a special exception, the copyright holders of PHYML give you permission to combine PHYML with free software programs or libraries that are released under the GNU LGPL and with code included in the standard release of PHYLIP under the University of Washington license (or modified versions of such code, with unchanged license). You may copy and distribute such a system following the terms of the GNU GPL for PHYML and the licenses of the other code concerned. . Note that people who make modified versions of PHYML are not obligated to grant this special exception for their modified versions; it is their choice whether to do so. The GNU General Public License gives permission to release a modified version without this exception; this exception also makes it possible to release a modified version which carries forward this exception. Files: csrc/dnapars.c csrc/protpars.c Copyright: © 1980-2008. University of Washington License: PHYLIP (c) Copyright 1980-2008. University of Washington. All rights reserved. Permission is granted to reproduce, perform, and modify these programs and documentation files. Permission is granted to distribute or provide access to these programs provided that this copyright notice is not removed, the programs are not integrated with or called by any product or service that generates revenue, and that your distribution of these documentation files and programs are free. Any modified versions of these materials that are distributed or accessible shall indicate that they are based on these programs. Institutions of higher education are granted permission to distribute this material to their students and staff for a fee to recover distribution costs. Permission requests for any other distribution of these program should be directed to license (at) u.washington.edu . Files: zconf.h Copyright: © 1995-1998 Jean-loup Gailly and Mark Adler License: zlib This software 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 software. . Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: . 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. . Jean-loup Gailly Mark Adler jloup@gzip.org madler@alumni.caltech.edu Files: debian/* Copyright: © 1999 Stephane Bortzmeyer © 2001 Dr. Guenter Bechly © 2001 Adrian Bunk © 2001 Doug Porter © 2002 Matej Vela © 2003 Colin Watson © 2003 Aaron M. Ucko © 2003 Brian R Furry © 2005 Steve Langasek © 2007 Nelson A. de Oliveira License: unknown The Copyright field above lists the developers who uploaded the package before this machine-readable file was assembled. . Please treat the contributions of Charles Plessy as if they were in the public domain. debian/upstream0000644000000000000000000000244111752427640010762 0ustar Contact: Manolo Gouy Documentation: http://pbil.univ-lyon1.fr/software/seaview_data/seaview Downloads: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/ Homepage: http://pbil.univ-lyon1.fr/software/seaview Name: SeaView Reference: - author: Gouy, Manolo and Guindon, Stephane and Gascuel, Olivier title: > SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building journal: Mol Biol Evol volume: 27 number: 2 pages: 221-224 year: 2010 PMID: 19854763 DOI: 10.1093/molbev/msp259 URL: http://mbe.oxfordjournals.org/cgi/content/abstract/27/2/221 eprint: http://mbe.oxfordjournals.org/cgi/reprint/27/2/221.pdf - Author: N. Galtier and M. Gouy and C. Gautier Title: SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny Journal: Comput. Applic. Biosci Volume: 12 Number: 6 Pages: 543-548 Year: 1996 PMID: 9021275 DOI: 10.1093/bioinformatics/12.6.543 URL: http://bioinformatics.oxfordjournals.org/content/12/6/543.abstract eprint: http://bioinformatics.oxfordjournals.org/content/12/6/543.full.pdf+html Screenshots: - http://pbil.univ-lyon1.fr/binaries/seaview4.png - http://pbil.univ-lyon1.fr/binaries/seaview-tree.png debian/clean0000644000000000000000000000002611575624045010202 0ustar *.o seaview seaviewps debian/rules0000755000000000000000000000070011725614742010254 0ustar #!/usr/bin/make -f # Same as upstream Makefile CFLAGS += -DUSE_XFT -I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF # Debian-specific names and paths CFLAGS += -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" export DEB_CFLAGS_MAINT_APPEND = $(CFLAGS) # Link as needed export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed # Hardening options # export DEB_BUILD_MAINT_OPTIONS = hardening=+all %: dh $@ debian/references0000644000000000000000000000170011326521310011222 0ustar @article{ManoloGouy10232009, author = {Gouy, Manolo and Guindon, Stephane and Gascuel, Olivier}, title = {{SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building}}, journal = {Mol Biol Evol}, volume = {}, number = {}, pages = {msp259}, doi = {10.1093/molbev/msp259}, year = {2009}, URL = {http://mbe.oxfordjournals.org/cgi/content/abstract/msp259v1}, eprint = {http://mbe.oxfordjournals.org/cgi/reprint/msp259v1.pdf} } @article{N.Galtier12011996, author = {Galtier, N. and Gouy, M. and Gautier, C.}, title = {{SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny}}, journal = {Comput. Appl. Biosci.}, volume = {12}, number = {6}, pages = {543-548}, doi = {10.1093/bioinformatics/12.6.543}, year = {1996}, URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/12/6/543}, eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/12/6/543.pdf} } debian/seaview.desktop0000644000000000000000000000161411110210632012211 0ustar # This file was orignially written for Debian, and can be copied, used, # modified and redistributed under the same licence as SeaView itself. [Desktop Entry] Version=1.0 Terminal=false Icon=seaview Exec=seaview %f Name=SeaView GenericName=Multiple sequence alignment editor GenericName[en]=Multiple sequence alignment editor GenericName[fr]=Éditeur d'alignements multiples de séquences GenericName[pt_BR]=Editor de alinhamento múltiplo de seqüências Comment=Edits multiple sequence alignments and prints them in PostScript format. Comment[en]=Edits multiple sequence alignments and prints them in PostScript format. Comment[fr]=Édite des aligmements multiples de séquences et les imprime au format PostScript. Comment[pt_BR]=Edita múltiplos alinhamentos de seqüências e os imprimem em formato PostScript. Type=Application Categories=Biology;Science;Education; MimeType=text/x-clustalw-alignment; debian/patches/0000755000000000000000000000000012202263633010614 5ustar debian/patches/use-dpkg-buildflags.patch0000644000000000000000000000120112033761366015470 0ustar Description: Allow users to override CFLAGS. Last-Update: Thu, 20 Sep 2012 13:16:04 +0900 Forwarded: Manolo Gouy --- seaview-4.3.3.orig/Makefile +++ seaview-4.3.3/Makefile @@ -29,7 +29,7 @@ #DEBUG = -g OPT = $(shell if [ '$(DEBUG)' = '' ]; then echo '-O3'; else echo '-O0'; fi) -CFLAGS = $(USE_XFT) -DFLTK1 -Dunix $(OPT) $(IFLTK) -I$(CSRC) -I. $(DEBUG) $(HELPFILE) $(PHYMLNAME) $(PDF_PS_FLAGS) +CFLAGS += $(USE_XFT) -DFLTK1 -Dunix $(OPT) $(IFLTK) -I$(CSRC) -I. $(DEBUG) $(HELPFILE) $(PHYMLNAME) $(PDF_PS_FLAGS) OBJECTS = seaview.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o \ debian/patches/add-ldl.patch0000644000000000000000000000066312202263633013143 0ustar Author: Andreas Tille LastChanged: Mon, 12 Aug 2013 13:03:12 +0200 Description: The build was lacking -ldl for successfull linking --- a/Makefile +++ b/Makefile @@ -17,7 +17,7 @@ FLTK = /usr/include #IFLTK = -I$(FLTK) #LFLTK = -L$(FLTK)/lib -EXTRALIBS = -lXft -lXext -lfontconfig -ljpeg -lpng -lXinerama $(LPDF) +EXTRALIBS = -lXft -lXext -lfontconfig -ljpeg -lpng -lXinerama $(LPDF) -ldl CC = gcc CXX = g++ debian/patches/series0000644000000000000000000000005112202263106012020 0ustar #use-dpkg-buildflags.patch add-ldl.patch debian/seaview.examples0000644000000000000000000000004311725463673012404 0ustar debian/example_files/* example.nxs debian/links0000644000000000000000000000010211702646747010240 0ustar usr/share/seaview/seaview.html usr/share/doc/seaview/seaview.html debian/watch0000644000000000000000000000015511411076373010223 0ustar version=3 opts="passive" \ ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_(.*)\.tar\.gz debian/changelog0000644000000000000000000004367112202264422011047 0ustar seaview (1:4.4.2-1) unstable; urgency=low * New upstream version Closes: #688632 * debian/control: - cme fix dpkg-control - anonscm in Vcs fields * debian/patches/add-ldl.patch: Provide lacking -ldl for successfull linking -- Andreas Tille Mon, 12 Aug 2013 13:03:12 +0200 seaview (1:4.4.0-1) unstable; urgency=low New upstream release using Clustal Omega instead of Clustal W. [ Andreas Tille ] * debian/rules: do not force hardening * debian/upstream: Keep old information from tasks file as additional citation [ Charles Plessy ] * debian/patches/use-dpkg-buildflags.patch: removed parts adopted upstream. * debian/control: recommend Clustal Omega instead of Clustal W. -- Charles Plessy Thu, 20 Sep 2012 13:30:40 +0900 seaview (1:4.3.3-3) unstable; urgency=low * debian/control: drop cdbs Build-Dependency * debian/rules: switch to short dh * debian/patches/use-dpkg-buildflags.patch: Patch for upstream Makefile to ensure hardening flags (Thanks to Simon Ruderich for the patch) Closes: #662818 * mv debian/examples debian/example_files because lintian claimed executable debhelper file (missinterpreting dir as debhelper input file) -- Andreas Tille Tue, 06 Mar 2012 20:38:53 +0100 seaview (1:4.3.3-2) unstable; urgency=low * Build on libpng-dev instead of libpng12-dev (Closes: #662499). * Harden through Debhelper's compatibility level 9. -- Charles Plessy Tue, 06 Mar 2012 13:47:02 +0900 seaview (1:4.3.3-1) unstable; urgency=low * New upstream release. * Include upstream example in Nexus format (debian/seaview.examples). * Complies with Policy 3.9.3 (debian/control, no other changes needed). -- Charles Plessy Fri, 24 Feb 2012 13:36:57 +0900 seaview (1:4.3.2-1) unstable; urgency=low * New upstream release. * Moved help file to /usr/share/seaview and left a symbolic link. -- Charles Plessy Sun, 08 Jan 2012 18:57:12 +0900 seaview (1:4.3.1-1) unstable; urgency=low * New upstream release incorporating debian/patches/format-security.patch. * Build seaview on armel architecture (debian/control). * Build-depend on libjpeg62-dev directly (debian/control), as libjpeg62-dev no more Provides libjpeg-dev since 6b1-2. -- Charles Plessy Sat, 03 Dec 2011 11:17:44 +0900 seaview (1:4.3.0-2) unstable; urgency=low * debian/patches/format-security.patch: Handle format strings properly Closes: #648121 * debian/control: Fix Vcs fields -- Andreas Tille Wed, 09 Nov 2011 08:26:27 +0100 seaview (1:4.3.0-1) unstable; urgency=low * New upstream version with SVG output. * Built on FLTK 1.3 (debian/control). * Corrected location of the help file (debian/rules). -- Charles Plessy Mon, 25 Jul 2011 18:57:42 +0900 seaview (1:4.2.12-1) unstable; urgency=low * New upstream versions. * Using Debhelper compatibility level 8 (debian/control, debian/compat). * Clean extra files through dh_clean (debian/clean, debian/rules). * Simplified build system using CDBS to pass options through CFLAGS, removing need for patching Makefile (debian/rules, debian/patches, debian/control). * Incremented Standards-Version to reflect conformance with Policy 3.9.2 (debian/control, no changes needed). -- Charles Plessy Fri, 10 Jun 2011 15:26:56 +0900 seaview (1:4.2.10-1) unstable; urgency=low * New upstream version * debian/patches/10_makefile.patch: - Linker flag -Wl,--as-needed to avoid useless linking and dependencies - Activate suggested Options in Makefile -- Andreas Tille Thu, 25 Nov 2010 18:30:25 +0100 seaview (1:4.2.9-1) unstable; urgency=low * New upstream version (Closes: #601244). -- Charles Plessy Wed, 27 Oct 2010 16:12:00 +0900 seaview (1:4.2.6-1) unstable; urgency=low * New upstream version. * Incremented Standards-Version to reflect conformance with Policy 3.9.1 (debian/control, no changes needed). * Refreshed debian/copyright according to latest DEP-5 discussions. * Moved debian/upstream-metadata.yaml's PMID and DOI keys in the Reference namespace. -- Charles Plessy Mon, 23 Aug 2010 14:30:30 +0900 seaview (1:4.2.5-1) unstable; urgency=low * New upstrem version * debian/watch: Force passive mode for ftp, because this works more reliably * Using dpkg source format version ‘3.0 (quilt)’ (debian/source/format) * debian/seaview.doc-base.reference: There is no docbase section Bibliography (even if this would be interesting) and thus it was moved to Science/Biology -- Andreas Tille Fri, 25 Jun 2010 11:56:05 +0200 seaview (1:4.2.4-1) unstable; urgency=low * New upstream release. * debian/control: - Incremented Standards-Version to reflect conformance with Policy 3.8.4 (no changes needed). - Support only i386 and amd64 until non-free autobuilders get more robust. * Updated bibliographic reference in ‘debian/upstream-metadata.yaml’. -- Charles Plessy Thu, 08 Apr 2010 13:07:41 +0900 seaview (1:4.2.1-1) unstable; urgency=low [ Charles Plessy ] * New upstream release that can be compiled with GCC 4.4.2 Closes: #560438, Thanks to Luk Claes for the help. * Updated bibliographic reference and Debian copyright file. [ Andreas Tille ] * s/Debian-Med/Debian Med/ in debian/control. -- Charles Plessy Wed, 06 Jan 2010 21:59:51 +0900 seaview (1:4.2-1) unstable; urgency=low * New upstream release. * debian/control: - Build depend on unversionned libjpeg-dev package. - Added XS-Autobuild: yes to benefit from the non-free autobuilders. - checked package conformance with Policy 3.8.3 (no changes needed). * Documented zlib.conf in debian/copyright. * Added various informations in debian/upstream-metadata.yaml. -- Charles Plessy Sun, 18 Oct 2009 17:10:08 +0900 seaview (1:4.1-1) unstable; urgency=low * New upstream version adding nucleotide ambiguity symbols in consensus DNA sequences. * debian/control: checked package conformance with Policy 3.8.2 and incremented Standards-Version accordingly (no changes needed). * debian/seaview.1*: accepted upstream and therefore deleted. -- Charles Plessy Mon, 13 Jul 2009 18:54:00 +0900 seaview (1:4.0-1) unstable; urgency=low * New upstream version - Computes and draws parsimony, distance and PhyML phylogenetic trees. - This new version unfortunately uses non-free files, and has therefore been removed from Debian, but is distributed in the ‘non-free’ section of its archive as a service its users. * debian/control: - Changed section to non-free/science. - Build-Depends on libxft-dev and libxext-dev. - Recommends phyml, muscle and clustalw. - Dropped dependency on xterm. - checked package conformance with Policy 3.8.1. - Updated description and removed reference from it. - Dropped build dependency on quilt. * debian/patches and debian/README.source removed: - 20-no-PDF-in-help.patch: upstream wording became true for Debian as well. - 21-location-of-seaview.help.patch: passing -DHELPFILENAME through debian/rules instead. - 40-seaview_align.sh-newline.patch, seaview_align-full_path.patch: seaview_align.sh was removed upstream. * debian/README.Debian deleted as well (obsolete). * debian/rules: - Makes `seaview' instead of `seaviewps' as (non-free) PDF support is not default anymore. - Indicate the location of the help file with: -DHELPFILENAME=\\\"/usr/share/doc/seaview/seaview.html\\\" - Uses `dh clean' and $(RM) macro in the clean target. - Uses `dh binary-arch` in the binary-arch target (created debian/docs, debian/seaview.examples, and debian/manpages). - Removed protein.mase from examples (removed upstream). - Removed patching facilities (no patches to apply anymore). * Removed `seaview_align.sh' from debian/install, as it was removed upstream. * debian/copyright: - Incremented year and version. - Link to the precise versions of the GNU GPL and LGPL. - Added the necessary disclaimers because SeaView became non-free. * Updated the manpage (debian/seaview.1*). * Registered the new help file with doc-base (debian/seaview.doc-base.help). -- Charles Plessy Wed, 27 May 2009 08:07:40 +0900 seaview (1:3.2-1) unstable; urgency=low * New upstream version: - Version 3.2: Database import can be done using a keyword. - Version 3.1: now use Fl_Native_File_Chooser. - Version 3.0: sequences can be imported from embl, genbank, swissprot if internet access. * debian/copyright: - Added the FL directory from Upstream sources. - Updated to the latest version of the machine-readable format. * debian/seaview.svg: vector icon made for SeaView and forwarded upstream. * debian/seaview.1*: added year 2008 to copyright statements. * Updated my email address. * debian/control, debian/compat: using Debhelper 7. * debian/control: added build-dependency on libpng12-dev and zlib1g-dev. * Experimental handling of bibliographic references: - debian/references contains a BibTeX-formatted reference. - debian/seaview.doc-base.references registers it for Doc-base in a "Bibliography" section to be proposed later. -- Charles Plessy Sun, 14 Dec 2008 22:58:57 +0900 seaview (1:2.4-1) unstable; urgency=low * New upstream version: - Version 2.3: corrected bug if adding/deleting/moving sequences when in 'view as proteins' mode. - Version 2.4: PHYLIP format: user can customize the max length of names. * debian/control: - Suggests: muscle, clustalw (non-free). Seaview detects if they are not present and grays the corresponding option. - Allows the upload by Debian Maintainers. - Checked that the package conforms to Policy 3.7.3. * debian/copyright: made machine-readable * MIME support: - debian/seaview.sharedmimeinfo associates .aln suffix and text/x-clustalw-alignment, debian/seaview.mime and debian/seaview.desktop associate seaview with this MIME type. - debian/rules executes dh_installmime. * debian/seaview.1.xml: increased version number to 2.4 (no other changes needed) * debian/seaview.1: rebuilt with DocBook XSL Stylesheets v1.73.2. -- Charles Plessy Sat, 12 Jan 2008 15:30:07 +0900 seaview (1:2.2-1) unstable; urgency=low [ Nelson A. de Oliveira ] * Updated watch file. [ Charles Plessy ] * New upstream release: - introduced interface to external alignment programs. - Work with several alignment windows; copy and paste sequence data between them. * Moved the Homepage: field out from the package's description. * Removed the XS- prefix of the Vcs fields in debian/control * Building the manpage offline: added seaview.1 to the package, and removed xsltproc, docbook-xml and docbook-xsl from the build-dependencies. * Patches to Seaview: - Refreshed. - Suppressed xterm_to_x-terminal-emulator.patch : strange communication problems happen between seaview and some terminal emulators, such as gnome-terminal or konsole. - Hardcoded the path to seaview_align.sh. -- Charles Plessy Sun, 18 Nov 2007 23:35:29 +0900 seaview (1:2.0-1) unstable; urgency=low * New upstream release. Use "Props:View as proteins" to align protein-coding DNA sequences. -- Charles Plessy Fri, 24 Aug 2007 00:02:33 +0900 seaview (20070615-1) unstable; urgency=low * New upstream release correcting problems with lowercase characters. * Converted the SVN repository which hosts the Debian source package to use the MergeWithUpstream option. * Moved examples to debian/examples. * Using 'quilt' as a patch management system instead of 'dpatch'. * Managing all the changes to the sources with quilt. * Adding $(misc-Depends) in debian/control. * Debian Menu transition: moving entry to Applications/Science/Biology. * Manpage: automatic date update; upgrading revision number. * Adding bibliographic reference to debian/copyright and debian/control. * Dropping 'config.h' patch from .diff.gz. -- Charles Plessy Sat, 21 Jul 2007 12:43:23 +0900 seaview (20070417-1) unstable; urgency=low * New upstream release adding processing of comments in FASTA format. -- Charles Plessy Sun, 29 Apr 2007 22:51:23 +0900 seaview (20070215-1) unstable; urgency=low * New upstream release, adding a new "Edit sequence" option in the Edit menu. * Updated manpage and converted it to Unicode. * Add Subversion repository URL to debian/control. * Including /usr/share/dpatch/dpatch.make in debian/rules. -- Charles Plessy Thu, 5 Apr 2007 09:38:08 +0900 seaview (20061005-1) unstable; urgency=low * New upstream release. The xpm icon and its sources are now included in. * New maintainer email: the previous one was not the intended mailing list. * Removing options passed to x-terminal-emulator if they are not a MUST in the policy chapter 11.8.3. * Improved manpage. -- Charles Plessy Sat, 28 Oct 2006 17:27:02 +0900 seaview (20060918-1) unstable; urgency=low * New upstream release (Closes: #357585) * Uses muscle instead of clustalw, therefore moving to main (Closes: #357587) * Update debian/copyright: the current licence of seaview is GPL (Closes: #357581) * Conforms to Standards version 3.7.2 and debhelper compatibility level 5. * Collective maintenance: Debian-Med Packaging Team is the new Maintainer. * Outputs PS instead of PDF as Debian can not support the PDFlib. * Uses x-terminal-emulator instead of xterm. * Support for freedesktop menus, and nice new icon. * Updated manpage. -- Charles Plessy Thu, 28 Sep 2006 12:13:53 +0900 seaview (20021127-4.1) unstable; urgency=medium * Non-maintainer upload. * Medium-urgency upload for RC bugfix. * Rebuild for the C++ ABI transition. Closes: #328175. -- Steve Langasek Thu, 22 Sep 2005 02:07:07 -0700 seaview (20021127-4) unstable; urgency=low * Cleaned up debian/rules file. * Conforms to Standards version 3.6.1. -- Brian R Furry Sun, 30 Nov 2003 00:04:02 +0000 seaview (20021127-3) unstable; urgency=low * Adopted by new maintainer; closes: 100261 * Conforms to Standards version 3.6.0. -- Brian R Furry Thu, 11 Sep 2003 21:12:40 -0400 seaview (20021127-2.2) unstable; urgency=low * NMU. * Downgrade dependency on clustalw to a recommendation, since we don't absolutely need it and it doesn't exist on mips(el). -- Aaron M. Ucko Tue, 17 Jun 2003 13:22:55 -0400 seaview (20021127-2.1) unstable; urgency=low * NMU. * Rebuild with Xft2-based FLTK (>= 1.1.3-2.1). -- Aaron M. Ucko Wed, 7 May 2003 20:36:02 -0400 seaview (20021127-2) unstable; urgency=low * QA upload. * Built with g++ 3.2 and libfltk1.1c102 (closes: #176147). -- Colin Watson Sat, 11 Jan 2003 02:50:11 +0000 seaview (20021127-1) unstable; urgency=low * QA upload. * New upstream release. * Conforms to Standards version 3.5.8. -- Matej Vela Sun, 1 Dec 2002 22:14:33 +0100 seaview (20021010-1) unstable; urgency=low * QA upload. * New upstream release. * Provide a config.h for old_file_chooser.cxx. * debian/menu: Use `section=Apps/Science hints=Biology' (see #162812). -- Matej Vela Sat, 19 Oct 2002 21:26:13 +0200 seaview (20020409-1) unstable; urgency=low * QA upload. * New upstream version (there's no version number in the sources). Closes: #128357. * align.cxx: - Handle temporary files securely (seaview 0.0 is not vulnerable). - Use x-terminal-emulator rather than xterm or rxvt. * seaview.1: - List NEXUS among the supported formats. - `-reducefonts' is no longer accepted. * Switched to debhelper 4. * Moved /usr/lib/seaview/seaview.help to /usr/share/seaview as architecture-independent. * Changed section from contrib/misc to contrib/science. * Added menu support. * debian/changelog: Remove obsolete Emacs local variables. * Conforms to Standards version 3.5.7. -- Matej Vela Fri, 20 Sep 2002 18:25:47 +0200 seaview (0.0-6.1) unstable; urgency=low * NMU * Update to build against XForms 0.89. (closes: Bug#118138) -- Doug Porter Mon, 12 Nov 2001 11:43:51 -0500 seaview (0.0-6) unstable; urgency=low * Maintainer set to Debian QA Group . -- Adrian Bunk Fri, 24 Aug 2001 23:58:22 +0200 seaview (0.0-5) unstable; urgency=low * Adopted by new maintainer; closes: #92802 * Moved all doc files to /usr/share/doc; closes: #91647 * Moved manpage to /usr/share/man; closes: #91064 * Updated to latest policy, and added Build-Depends. * Removed some unnecessary files in debian dir. -- Dr. Guenter Bechly Sat, 7 Apr 2001 18:00:30 +0200 seaview (0.0-4) unstable; urgency=low * A few examples added * New bug in seaview_align.sh, this time fixed seriously. -- Stephane Bortzmeyer Thu, 3 Jun 1999 10:07:55 +0200 seaview (0.0-3) unstable; urgency=low * Big bug in seaview_align.sh (not all parameters were passed). -- Stephane Bortzmeyer Wed, 26 May 1999 14:39:26 +0200 seaview (0.0-2) unstable; urgency=low * No longer depends on c-shell or xterm. Closes #34700 * Manual page. Closes #34615 -- Stephane Bortzmeyer Tue, 25 May 1999 14:42:15 +0200 seaview (0.0-1) unstable; urgency=low * Initial Release. -- Stephane Bortzmeyer Mon, 1 Mar 1999 16:41:51 +0100 debian/seaview.doc-base.help0000644000000000000000000000044011204030730013143 0ustar Document: seaview-help Title: SeaView help Author: Manolo Gouy Abstract: This is the hypertext help available when running SeaView. Section: Science/Biology Format: HTML Index: /usr/share/doc/seaview/seaview.html Files: /usr/share/doc/seaview/seaview.html debian/seaview.mime0000644000000000000000000000017711110210632011472 0ustar text/x-clustalw-alignment; seaview -save clustal '%s'; description=Clustal W multiple sequence alignment; nametemplate=%s.aln debian/seaview.doc-base.reference0000644000000000000000000000021111411077033014154 0ustar Document: seaview-reference Title: Reference for SeaView Section: Science/Biology Format: Text Files: /usr/share/doc/seaview/references debian/seaview.sharedmimeinfo0000644000000000000000000000100111110210632013520 0ustar Multiple sequence alignment in Clustal W format Alignement multiple de séquences au format Clustal W debian/compat0000644000000000000000000000000211725447705010400 0ustar 9 debian/seaview.svg0000644000000000000000000001163511112454020011346 0ustar image/svg+xml S E A - debian/control0000644000000000000000000000327412202142115010565 0ustar Source: seaview Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: non-free/science Priority: optional Build-Depends: debhelper (>= 9), libfltk1.3-dev, libjpeg62-dev, libpng-dev, libxft-dev, libxext-dev, libxinerama-dev, zlib1g-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/seaview/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/seaview/trunk/ Homepage: http://pbil.univ-lyon1.fr/software/seaview.html XS-Autobuild: yes Package: seaview Architecture: i386 amd64 armel Depends: ${shlibs:Depends}, ${misc:Depends} Recommends: clustalo, muscle, phyml Description: Multiplatform interface for sequence alignment and phylogeny SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees. Alignments can be manually edited. It drives the programs Muscle or Clustal Omega for multiple sequence alignment, and also allows one to use any external alignment algorithm able to read and write FASTA-formatted files. It computes phylogenetic trees by parsimony using PHYLIP's dnapars/protpars algorithm, by distance with NJ or BioNJ algorithms on a variety of evolutionary distances, or by maximum likelihood using the program PhyML 3.0. SeaView draws phylogenetic trees on screen or PostScript files, and allows one to download sequences from EMBL/GenBank/UniProt using the Internet.