debian/0000755000000000000000000000000011726073221007167 5ustar debian/upstream0000644000000000000000000000073011726061715010757 0ustar Contact: Christopher Lee Name: POA Reference: author: Grasso, Catherine and Lee, Christopher title: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems journal: Bioinformatics volume: 20 number: 10 pages: 1546-1556 year: 2004 DOI: 10.1093/bioinformatics/bth126 PMID: 14962922 URL: http://bioinformatics.oxfordjournals.org/content/20/10/1546 debian/examples0000644000000000000000000000001511726062653010733 0ustar multidom.seq debian/poa.1.xml0000644000000000000000000002427511110210225010621 0ustar Charles"> Plessy"> september 26, 2006"> 1"> charles-debian-nospam@plessy.org"> POA"> Debian"> GNU"> GPL"> ]>
&dhemail;
2006 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; align a set of sequences or alignments. &dhpackage; OPTIONS MATRIXFILE One of the , , or arguments must be used, since a sequence or alignment file is required. DESCRIPTION POA is Partial Order Alignment, a fast program for multiple sequence alignment (MSA) in bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment. Partial order alignment is an approach to MSA, which can be combined with existing methods such as progressive alignment. POA optimally aligns a pair of MSAs and which therefore can be applied directly to progressive alignment methods such as CLUSTAL. For large alignments, Progressive POA is 10 to 30 times faster than CLUSTALW. EXAMPLES poa multidom.seq m.aln blosum80.mat On Debian systems, poa can be tested using the following command: poa /usr/share/doc/poa/examples/multidom.seq /dev/stdout /usr/share/poa/blosum80.mat OPTIONS INPUT FILE Read in FASTA sequence file. FILE Read in MSA alignment file. FILE Read in second MSA file. FILE Filter MSA to include list of seqs in file. FILE Filter second MSA to include list of seqs in file. FILE Filter MSA to include list of seqs in file. FILE Filter second MSA to include list of seqs in file. FILE Read an MSA from each filename listed in file. Force FASTA/MSA sequences to lowercase (nucleotides in our matrix files). Force FASTA/MSA sequences to UPPERCASE (amino acids in our matrix files). ALIGNMENT Do global alignment. Perform progressive alignment using a guide tree built by neighbor joining from a set of sequence-sequence similarity scores. FILE Read tab-delimited file of similarity scores (If not provided, scores are constructed using pairwise sequence alignment.) Fuse identical letters on align rings. ANALYSIS Perform heaviest bundling to generate consensi. VALUE Include in heaviest bundle sequences with percent ID (as a fraction) >= VALUE. OUTPUT FILE Write out MSA in PIR format. FILE Write out MSA in CLUSTAL format. FILE Write out MSA in PO format. Write out MSA with sequences in their input order. LETTERS Print score matrix to stdout. Restrict MSA output to heaviest bundles (PIR only). Run in verbose mode (e.g. output gap penalties). REFERENCE Please cite Grasso C, Lee C. (2004) Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics. 2004 Jul 10;20(10):1546-56. Epub 2004 Feb 12. SEE ALSO The homepage of POA is http://www.bioinformatics.ucla.edu/poa COPYRIGHTS Copyright (C) 2001, 2006 Christopher Lee leec@mbi.ucla.edu. POA 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. This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/test/0000755000000000000000000000000011726071140010144 5ustar debian/test/multidom.clustal0000644000000000000000000002365111726071012013374 0ustar CLUSTAL W (1.74) multiple sequence alignment ABL1_HUMAN MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNS CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN KENLLAGPSENDPNLF---VALYDFVASGDN------------------- CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN ----------------MEAIAKYDFKATADD------------------- MATK_HUMAN -------------------------------MAGRGSLVSWRAFHGCDSA ABL1_HUMAN ----------------------------------------------TLSI CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN ----------------------------------------------ELSF MATK_HUMAN EELPRVSPRFLRAWHPPPVSARMPTRRWAPGTQCITKCEHTRPKPGELAF ABL1_HUMAN TKGEKLRVLGYNHN-GEWCEAQTK-NGQ-GWVPSNYITPV------NSLE CRKL_HUMAN ----------------------------------------MSSARFDSSD GRB2_HUMAN KRGDILKVLNEECD-QNWYKAEL--NGKDGFIPKNYI----------EMK MATK_HUMAN RKGDVVTIL-EACENKSWYRVKHHTSGQEGLLAAGALRER------EALS ABL1_HUMAN KHS------WYHGPVSRNAAEYLLSSGIN-GSFLVRESESSPGQRSISLR CRKL_HUMAN RSA------WYMGPVSRQEAQTRLQGQRH-GMFLVRDSSTCPGDYVLSVS GRB2_HUMAN PHP------WFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVK MATK_HUMAN ADPKLSLMPWFHGKISGQEAVQQLQ-PPEDGLFLVRESARHPGDYVLCVS ABL1_HUMAN YEGRVYHYRINTASDGKLYVSSESRFNTLAELVHHHSTVADGLITTLHYP CRKL_HUMAN ENSRVSHYIINSLPNRRFKIGDQE-FDHLPALLEFYK-IHYLDTTTLIEP GRB2_HUMAN FGNDVQHFKVLRDGAGK-YFLWVVKFNSLNELVDYHRS------TSV--- MATK_HUMAN FGRDVIHYRV-LHRDGHLTIDEAVFFCNLMDMVEHYSKDKGAICTKLVRP ABL1_HUMAN APKRNKPTVYGVS-PNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYS CRKL_HUMAN APRYPSPPMGSVSAPN---------------------------------- GRB2_HUMAN --SRNQ-QIF-LR--D---------------------------------- MATK_HUMAN --KRKHGTKSAEEELARAGWLLNLQHLTLGAQIGEGEFGAVLQGEY--LG ABL1_HUMAN LTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIIT CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN QKVAVKNIKCDVT-AQAFLDETAVMTKMQHENLVRLLGVILHQG-LYIVM ABL1_HUMAN EFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLA CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN EHVSKGNLVNFLRTRGRALVNTAQLLQFSLHVAEGMEYLESKKLVHRDLA ABL1_HUMAN ARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNK CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN ARNILVSEDLVAKVSDFGLAK---AERKGLDS-SRLPVKWTAPEALKHGK ABL1_HUMAN FSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCP CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN FTSKSDVWSFGVLLWEVFSYGRAPYPKMSLKEVSEAVEKGYRMEPPEGCP ABL1_HUMAN EKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKELGKQGV CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN GPVHVLMSSCWEAEPARRPPF----------------------------- ABL1_HUMAN RGAVSTLLQAPELPTKTRTSRRAAEHRDTTDVPEMPHSKGQGESDPLDHE CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN PAVSPLLPRKERGPPEGGLNEDERLLPKDKKTNLFSALIKKKKKTAPTPP CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN KRSSSFREMDGQPERRGAGEEEGRDISNGALAFTPLDTADPAKSPKPSNG CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN AGVPNGALRESGGSGFRSPHLWKKSSTLTSSRLATGEEEGGGSSSKRFLR CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN SCSASCVPHGAKDTEWRSVTLPRDLQSTGRQFDSSTFGGHKSEKPALPRK CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN RAGENRSDQVTRGTVTPPPRLVKKNEEAADEVFKDIMESSPGSSPPNLTP CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN KPLRRQVTVAPASGLPHKEEAEKGSALGTPAAAEPVTPTSKAGSGAPGGT CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN SKGPAEESRVRRHKHSSESPGRDKGKLSRLKPAPPPPPAASAGKAGGKPS CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN QSPSQEAAGEAVLGAKTKATSLVDAVNSDAAKPSQPGEGLKKPVLPATPK CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN PQSAKPSGTPISPAPVPSTLPSASSALAGDQPSSTAFIPLISTRVSLRKT CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN RQPPERIASGAITKGVVLDSTEALCLAISRNSEQMASHSAVLEAGKNLYT CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN FCVSYVDSIQQMRNKFAFREAINKLENNLRELQICPATAGSGPAATQDFS CRKL_HUMAN -------------------------------------------------- GRB2_HUMAN -------------------------------------------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN KLLSSVKEISDIVQR----------------------------------- CRKL_HUMAN ---------------LPTAEDNLEYVRTLYDF-PGNDAEDLPFKKGEILV GRB2_HUMAN ---------------IEQVPQQPTYVQALFDFDPQEDGE-LGFRRGDFIH MATK_HUMAN -------------------------------------------------- ABL1_HUMAN -------------------------------------------------- CRKL_HUMAN IIEKPEEQWWSARNKDGRVGMIPVPYVEKLVRSSPHGKHGNRNSNSYGIP GRB2_HUMAN VMDNSDPNWWKGACH-GQTGMFPRNYVTPVNRN----------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN -------------------------------------------------- CRKL_HUMAN EPAHAYAQPQTTTPLPAVSGSPGAAITPLPSTQNGPVFAKAIQKRVPCAY GRB2_HUMAN -------------------------------------------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN -------------------------------------------------- CRKL_HUMAN DKTALALEVGDIVKVTRMNINGQWEGEVNGRKGLFPFTHVKIFDPQNPDE GRB2_HUMAN -------------------------------------------------- MATK_HUMAN -------------------------------------------------- ABL1_HUMAN --------------------------------------- CRKL_HUMAN NE------------------------------------- GRB2_HUMAN --V------------------------------------ MATK_HUMAN ---RKLAEKLARELRSAGAPASVSGQDADGSTSPRSQEP debian/source/0000755000000000000000000000000011726063335010474 5ustar debian/source/format0000644000000000000000000000001411301174376011677 0ustar 3.0 (quilt) debian/docs0000644000000000000000000000000711726062633010044 0ustar README debian/copyright0000644000000000000000000000241611726065012011124 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: POA Upstream-Contact: Christopher Lee Source: http://sourceforge.net/projects/poamsa/files/poamsa/2.0/ Files: * Copyright: 2004-2006 Christopher Lee License: GPL2+ This package 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 package 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 package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. Files: debian/* Copyright: 2006 Charles Plessy , 2012 Andreas Tille License: GPL-2+ Same as software itself. debian/compat0000644000000000000000000000000211726062227010371 0ustar 9 debian/install0000644000000000000000000000015611110210225010542 0ustar poa /usr/bin blosum80.mat /usr/share/poa blosum80_trunc.mat /usr/share/poa make_pscores.pl /usr/share/poa debian/control0000644000000000000000000000231011726062223010566 0ustar Source: poa Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Charles Plessy , Andreas Tille Build-Depends: debhelper (>= 9) Standards-Version: 3.9.3 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/poa/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/poa/trunk/ Homepage: http://poamsa.sourceforge.net/ Package: poa Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: blast2 Enhances: t-coffee Description: Partial Order Alignment for multiple sequence alignment POA is Partial Order Alignment, a fast program for multiple sequence alignment (MSA) in bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment. Partial order alignment is an approach to MSA, which can be combined with existing methods such as progressive alignment. POA optimally aligns a pair of MSAs and which therefore can be applied directly to progressive alignment methods such as CLUSTAL. For large alignments, Progressive POA is 10-30 times faster than CLUSTALW. debian/README.Debian0000644000000000000000000000107611726061471011240 0ustar poa for Debian -------------- POA needs a matrix file to operate. The matrices shipped in the sources of POA can be found in /usr/share/poa/. You can test POA with the following command: poa -read_fasta /usr/share/doc/poa/examples/multidom.seq -clustal /dev/stdout -v /usr/share/poa/blosum80.mat The original POA archive contains a perl script called "make_pscores.pl", which can be found in /usr/share/poa. To use it, you need the blastall program, provided by the Debian package "blast2". -- Charles Plessy , Tue, 28 September 2006 debian/manpages0000644000000000000000000000001311540705460010700 0ustar debian/*.1 debian/watch0000644000000000000000000000015311110210225010177 0ustar version=3 opts="uversionmangle=s/$/.0/,dversionmangle=s/\+.*$//" \ http://sf.net/poamsa/ poaV(.*)\.tar\.gz debian/dirs0000644000000000000000000000002611110210225010031 0ustar usr/bin usr/share/poa debian/changelog0000644000000000000000000000432511726073221011045 0ustar poa (2.0+20060928-3) unstable; urgency=low [ Charles Plessy ] * Updated my email address. [ David Paleino ] * Removed myself from Uploaders [ Charles Plessy ] * Documented information in ‘debian/upstream’. * Removed mention of the bibliographic reference in ‘debian/control’. [ Andreas Tille ] * debian/upstream: - Fixed URLs - Moved DOI/PMID to References - Removed (wrong Homepage) - Removed watch * debian/control: - Former homepage does not work any more, use Sourceforge page as homepage - Fixed VCS fields - Standards-Version: 3.9.3 (no changes needed) * debian/source/format: 3.0 (quilt) * debhelper 9 (control+compat) * debian/copyright: Rewritten to fit DEP5 and verified using cme fix dpkg-copyright * debian/rules + debhelper files: - use short dh - do not try to redirect output of test to stdout which breaks inside pbuilder * debian/test/multidom.clustal: Store result of proposed test and compare in dh_auto_test target -- Andreas Tille Thu, 08 Mar 2012 08:39:05 +0100 poa (2.0+20060928-2) unstable; urgency=low [ Charles Plessy ] * debian/control: - Add Subversion repository URL to debian/control. - Moved the Homepage: field out from the package's description. - Enhances: t-coffee. [ Nelson A. de Oliveira ] * Added watch file. [ David Paleino ] * debian/poa.1 added - statically built * debian/control: - B-D updated - added myself to Uploaders - moved XS-Vcs-* to Vcs-* - Updated to Standards-Version 3.7.3 (no changes needed) * debian/rules: - statically build manpages (target poa.1 available) - minor changes [ Andreas Tille ] * Added myself to uploaders -- Andreas Tille Fri, 21 Mar 2008 23:41:56 +0100 poa (2.0+20060928-1) unstable; urgency=low * New upstream version. THE PREVIOUS VERSION WAS NOT 2.0. * Updated manpage. * Added a test rule. * Removed the watch file. -- Charles Plessy Thu, 28 Sep 2006 10:21:43 +0900 poa (2.0-1) unstable; urgency=low * Initial release Closes: #378288 -- Charles Plessy Sun, 20 Aug 2006 11:21:24 +0900 debian/rules0000755000000000000000000000133011726072077010254 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 PKG := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') %: dh $@ DB2MAN=/usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl XP=xsltproc \ -o debian/ \ -''-nonet $(PKG).1: debian/$(PKG).1.xml $(XP) $(DB2MAN) $< override_dh_auto_build: $(MAKE) poa override_dh_auto_test: tmpfile=`mktemp` ; \ ./$(PKG) -read_fasta multidom.seq -clustal $$tmpfile -v blosum80.mat ; \ if cmp $$tmpfile $(CURDIR)/debian/test/multidom.clustal ; then \ echo "Test passed" ; \ rm -f $$tmpfile ; \ else \ echo "TEST FAILED!!!" ; \ echo "File $$tmpfile is different from $(CURDIR)/multidom.clustal" ; \ exit 1 ; \ fi debian/poa.10000644000000000000000000001127711110210225010020 0ustar .\" Title: POA .\" Author: .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: september 26, 2006 .\" Manual: .\" Source: .\" .TH "POA" "1" "september 26, 2006" "" "" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" poa - align a set of sequences or alignments. .SH "SYNOPSIS" .HP 4 \fBpoa\fR [OPTIONS] [\fIMATRIXFILE\fR] .PP One of the \fB\-read_fasta\fR, \fB\-read_msa\fR, or \fB\-read_msa_list\fR arguments must be used, since a sequence or alignment file is required\. .SH "DESCRIPTION" .PP \fBPOA\fR is Partial Order Alignment, a fast program for multiple sequence alignment (MSA) in bioinformatics\. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment\. Partial order alignment is an approach to MSA, which can be combined with existing methods such as progressive alignment\. POA optimally aligns a pair of MSAs and which therefore can be applied directly to progressive alignment methods such as CLUSTAL\. For large alignments, Progressive POA is 10 to 30 times faster than CLUSTALW\. .SH "EXAMPLES" .PP \fBpoa\fR \fB\-read_fasta\fR \fImultidom\.seq\fR \fB\-clustal\fR \fIm\.aln\fR \fIblosum80\.mat\fR .PP On Debian systems, \fBpoa\fR can be tested using the following command: .PP \fBpoa\fR \fB\-read_fasta\fR \fI/usr/share/doc/poa/examples/multidom\.seq\fR \fB\-clustal\fR \fI/dev/stdout\fR \fB\-v\fR \fI/usr/share/poa/blosum80\.mat\fR .SH "OPTIONS" .SS "INPUT" .PP \fB\-read_fasta\fR \fIFILE\fR .RS 4 Read in FASTA sequence file\. .RE .PP \fB\-read_msa\fR \fIFILE\fR .RS 4 Read in MSA alignment file\. .RE .PP \fB\-read_msa2\fR \fIFILE\fR .RS 4 Read in second MSA file\. .RE .PP \fB\-subset\fR \fIFILE\fR .RS 4 Filter MSA to include list of seqs in file\. .RE .PP \fB\-subset2\fR \fIFILE\fR .RS 4 Filter second MSA to include list of seqs in file\. .RE .PP \fB\-remove\fR \fIFILE\fR .RS 4 Filter MSA to include list of seqs in file\. .RE .PP \fB\-remove2\fR \fIFILE\fR .RS 4 Filter second MSA to include list of seqs in file\. .RE .PP \fB\-read_msa_list\fR \fIFILE\fR .RS 4 Read an MSA from each filename listed in file\. .RE .PP \fB\-tolower\fR .RS 4 Force FASTA/MSA sequences to lowercase (nucleotides in our matrix files)\. .RE .PP \fB\-toupper\fR .RS 4 Force FASTA/MSA sequences to UPPERCASE (amino acids in our matrix files)\. .RE .SS "ALIGNMENT" .PP \fB\-do_global\fR .RS 4 Do global alignment\. .RE .PP \fB\-do_progressive\fR .RS 4 Perform progressive alignment using a guide tree built by neighbor joining from a set of sequence\-sequence similarity scores\. .RE .PP \fB\-read_pairscores\fR \fIFILE\fR .RS 4 Read tab\-delimited file of similarity scores (If not provided, scores are constructed using pairwise sequence alignment\.) .RE .PP \fB\-fuse_all\fR .RS 4 Fuse identical letters on align rings\. .RE .SS "ANALYSIS" .PP \fB\-hb\fR .RS 4 Perform heaviest bundling to generate consensi\. .RE .PP \fB\-hbmin\fR \fIVALUE\fR .RS 4 Include in heaviest bundle sequences with percent ID (as a fraction) >= \fIVALUE\fR\. .RE .SS "OUTPUT" .PP \fB\-pir\fR \fIFILE\fR .RS 4 Write out MSA in PIR format\. .RE .PP \fB\-clustal\fR \fIFILE\fR .RS 4 Write out MSA in CLUSTAL format\. .RE .PP \fB\-po\fR \fIFILE\fR .RS 4 Write out MSA in PO format\. .RE .PP \fB\-preserve_seqorder\fR .RS 4 Write out MSA with sequences in their input order\. .RE .PP \fB\-printmatrix\fR \fILETTERS\fR .RS 4 Print score matrix to stdout\. .RE .PP \fB\-best\fR .RS 4 Restrict MSA output to heaviest bundles (PIR only)\. .RE .PP \fB\-v\fR .RS 4 Run in verbose mode (e\.g\. output gap penalties)\. .RE .SH "REFERENCE" .PP Please cite Grasso C, Lee C\. (2004) Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems\. Bioinformatics\. 2004 Jul 10;20(10):1546\-56\. Epub 2004 Feb 12\. .SH "SEE ALSO" .PP The homepage of POA is \fIhttp://www\.bioinformatics\.ucla\.edu/poa\fR .SH "COPYRIGHTS" .PP Copyright (C) 2001, 2006 Christopher Lee \. POA 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\. .PP This manual page was written by Charles Plessy for the Debian(TM) system (but may be used by others)\. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation\. .PP On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common\-licenses/GPL\. .SH "COPYRIGHT" Copyright \(co 2006 Charles Plessy .br debian/NEWS0000644000000000000000000000104311110210225007644 0ustar poa (2.0+20060928-1) unstable; urgency=low The Debian package version 2.0-1 was built on the upstream sources "poa_release_2_0.tar.gz" which unfortunately contained an earlier 1.x version of poa. The new Debian package version 2.0+20060928-1 is thus a major upgrade. In its version 2.0, poa does not support the same file formats as before. Please refer to the documentation of poa to check wether the options you used before are still existing. -- Charles Plessy Thu, 28 Sep 2006 10:19:33 +0900