--- poa-2.0+20060928.orig/debian/poa.1
+++ poa-2.0+20060928/debian/poa.1
@@ -0,0 +1,192 @@
+.\" Title: POA
+.\" Author:
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" 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
+<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\.
+.PP
+This manual page was written by Charles Plessy
+<charles\-debian\-nospam@plessy\.org>
+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
--- poa-2.0+20060928.orig/debian/rules
+++ poa-2.0+20060928/debian/rules
@@ -0,0 +1,71 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Build rules for the Debian package poa
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+# Modifications by Charles Plessy during the year 2006
+# are hereby released as "public domain"
+
+PROGRAM_NAME = poa
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+DB2MAN=/usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl
+XP=xsltproc \
+ -o debian/ \
+ -''-nonet
+
+$(PROGRAM_NAME).1: debian/$(PROGRAM_NAME).1.xml
+ $(XP) $(DB2MAN) $<
+
+build-stamp: build
+build:
+ dh_testdir
+ $(MAKE) $(PROGRAM_NAME)
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+ [ ! -f Makefile ] || $(MAKE) clean
+ dh_clean
+
+test:
+ ./poa -read_fasta multidom.seq -clustal /dev/stdout -v blosum80.mat
+
+install: build-stamp
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+binary-indep: build install
+
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs README
+ dh_installexamples multidom.seq
+ dh_install
+ dh_installman debian/$(PROGRAM_NAME).1
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
--- poa-2.0+20060928.orig/debian/compat
+++ poa-2.0+20060928/debian/compat
@@ -0,0 +1 @@
+5
--- poa-2.0+20060928.orig/debian/dirs
+++ poa-2.0+20060928/debian/dirs
@@ -0,0 +1,2 @@
+usr/bin
+usr/share/poa
--- poa-2.0+20060928.orig/debian/README.Debian
+++ poa-2.0+20060928/debian/README.Debian
@@ -0,0 +1,15 @@
+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 <charles-debian-nospam@plessy.org>, Tue, 28 September 2006
--- poa-2.0+20060928.orig/debian/changelog
+++ poa-2.0+20060928/debian/changelog
@@ -0,0 +1,42 @@
+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 <tille@debian.org> 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 <charles-debian-nospam@plessy.org> Thu, 28 Sep 2006 10:21:43 +0900
+
+poa (2.0-1) unstable; urgency=low
+
+ * Initial release Closes: #378288
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org> Sun, 20 Aug 2006 11:21:24 +0900
+
--- poa-2.0+20060928.orig/debian/copyright
+++ poa-2.0+20060928/debian/copyright
@@ -0,0 +1,32 @@
+This package was debianized by Charles Plessy
+<charles-debian-nospam@plessy.org> on Sun, 20 Aug 2006 11:21:24 +0900. The
+packaging work is in the public domain unless stated otherwise. The manpage for
+poa and its source are licenced under the GPL.
+
+It was downloaded from http://sourceforge.net/project/showfiles.php?group_id=168080&package_id=191162&release_id=418237
+
+Copyright 2001, 2006 Christopher Lee <leec@mbi.ucla.edu>
+
+The project page on the SourceForge website indicates that this program is
+licenced under the GNU General Public Licence.
+(see: http://sourceforge.net/projects/poamsa/)
+
+License:
+
+ 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'.
+
--- poa-2.0+20060928.orig/debian/install
+++ poa-2.0+20060928/debian/install
@@ -0,0 +1,4 @@
+poa /usr/bin
+blosum80.mat /usr/share/poa
+blosum80_trunc.mat /usr/share/poa
+make_pscores.pl /usr/share/poa
--- poa-2.0+20060928.orig/debian/NEWS
+++ poa-2.0+20060928/debian/NEWS
@@ -0,0 +1,10 @@
+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 <charles-debian-nospam@plessy.org> Thu, 28 Sep 2006 10:19:33 +0900
--- poa-2.0+20060928.orig/debian/watch
+++ poa-2.0+20060928/debian/watch
@@ -0,0 +1,3 @@
+version=3
+opts="uversionmangle=s/$/.0/,dversionmangle=s/\+.*$//" \
+http://sf.net/poamsa/ poaV(.*)\.tar\.gz
--- poa-2.0+20060928.orig/debian/poa.1.xml
+++ poa-2.0+20060928/debian/poa.1.xml
@@ -0,0 +1,326 @@
+<?xml version='1.0' encoding='ISO-8859-1'?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
+
+
+ <!ENTITY dhfirstname "<firstname>Charles</firstname>">
+ <!ENTITY dhsurname "<surname>Plessy</surname>">
+ <!ENTITY dhdate "<date>september 26, 2006</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>charles-debian-nospam@plessy.org</email>">
+ <!ENTITY dhusername "Charles Plessy">
+ <!ENTITY dhucpackage "<refentrytitle>POA</refentrytitle>">
+ <!ENTITY dhpackage "poa">
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<!-- Copyright 2006 Charles Plessy. You can use, copy, and redistribute this manpage under the GNU GPL. -->
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+<!-- <author>
+ &dhfirstname;
+ &dhsurname;
+ </author> -->
+ <copyright>
+ <year>2006</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>align a set of sequences or alignments.</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt">OPTIONS</arg>
+ <arg choice="opt">
+ <replaceable>MATRIXFILE</replaceable>
+ </arg>
+ </cmdsynopsis>
+
+ <para>One of the <option>-read_fasta</option>, <option>-read_msa</option>, or <option>-read_msa_list</option> arguments must be used, since a sequence or alignment file is required.</para>
+
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+
+ <para><command>POA</command> 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.</para>
+ </refsect1>
+
+ <refsect1>
+ <title>EXAMPLES</title>
+ <para><command>poa</command> <option>-read_fasta</option> <filename>multidom.seq</filename> <option>-clustal</option> <filename>m.aln</filename> <filename>blosum80.mat</filename></para>
+ <para>On Debian systems, <command>poa</command> can be tested using the following command:</para>
+ <para><command>poa</command> <option>-read_fasta</option> <filename>/usr/share/doc/poa/examples/multidom.seq</filename> <option>-clustal</option> <filename>/dev/stdout</filename> <option>-v</option> <filename>/usr/share/poa/blosum80.mat</filename></para>
+ </refsect1>
+
+ <refsect1>
+ <title>OPTIONS</title>
+ <refsect2>
+ <title>INPUT</title>
+ <variablelist>
+ <varlistentry>
+ <term><option>-read_fasta</option>
+ <parameter>FILE</parameter>
+ </term>
+ <listitem>
+ <para>Read in FASTA sequence file.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-read_msa</option>
+ <parameter>FILE</parameter>
+ </term>
+ <listitem>
+ <para>Read in MSA alignment file.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-read_msa2</option>
+ <parameter>FILE</parameter>
+ </term>
+ <listitem>
+ <para>Read in second MSA file.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-subset</option>
+ <parameter>FILE</parameter>
+ </term>
+ <listitem>
+ <para>Filter MSA to include list of seqs in file.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-subset2</option>
+ <parameter>FILE</parameter>
+ </term>
+ <listitem>
+ <para>Filter second MSA to include list of seqs in file.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-remove</option>
+ <parameter>FILE</parameter>
+ </term>
+ <listitem>
+ <para>Filter MSA to include list of seqs in file.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-remove2</option>
+ <parameter>FILE</parameter>
+ </term>
+ <listitem>
+ <para>Filter second MSA to include list of seqs in file.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-read_msa_list</option>
+ <parameter>FILE</parameter>
+ </term>
+ <listitem>
+ <para>Read an MSA from each filename listed in file.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-tolower</option>
+ </term>
+ <listitem>
+ <para>Force FASTA/MSA sequences to lowercase (nucleotides in our matrix files).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-toupper</option>
+ </term>
+ <listitem>
+ <para>Force FASTA/MSA sequences to UPPERCASE (amino acids in our matrix files).</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect2>
+
+ <refsect2>
+ <title>ALIGNMENT</title>
+
+ <variablelist>
+ <varlistentry>
+ <term><option>-do_global</option></term>
+ <listitem>
+ <para>Do global alignment.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-do_progressive</option></term>
+ <listitem>
+ <para>Perform progressive alignment using a guide tree built by neighbor joining from a set of sequence-sequence similarity scores.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-read_pairscores</option>
+ <parameter>FILE</parameter>
+ </term>
+ <listitem>
+ <para>Read tab-delimited file of similarity scores (If not provided, scores are constructed using pairwise sequence alignment.)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-fuse_all</option>
+ </term>
+ <listitem>
+ <para>Fuse identical letters on align rings.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect2>
+
+ <refsect2>
+ <title>ANALYSIS</title>
+
+ <variablelist>
+ <varlistentry>
+ <term><option>-hb</option>
+ </term>
+ <listitem>
+ <para>Perform heaviest bundling to generate consensi.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-hbmin</option>
+ <parameter>VALUE</parameter>
+ </term>
+ <listitem>
+ <para>Include in heaviest bundle sequences with percent ID (as a fraction) >= <parameter>VALUE</parameter>.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect2>
+
+ <refsect2>
+ <title>OUTPUT</title>
+
+ <variablelist>
+ <varlistentry>
+ <term><option>-pir</option>
+ <parameter>FILE</parameter>
+ </term>
+ <listitem>
+ <para>Write out MSA in PIR format.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-clustal</option>
+ <parameter>FILE</parameter>
+ </term>
+ <listitem>
+ <para>Write out MSA in CLUSTAL format.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-po</option>
+ <parameter>FILE</parameter>
+ </term>
+ <listitem>
+ <para>Write out MSA in PO format.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-preserve_seqorder</option></term>
+ <listitem>
+ <para>Write out MSA with sequences in their input order.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-printmatrix</option>
+ <parameter>LETTERS</parameter>
+ </term>
+ <listitem>
+ <para>Print score matrix to stdout.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-best</option>
+ </term>
+ <listitem>
+ <para>Restrict MSA output to heaviest bundles (PIR only).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-v</option>
+ <option></option>
+ </term>
+ <listitem>
+ <para>Run in verbose mode (e.g. output gap penalties).</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect2>
+ </refsect1>
+
+ <refsect1>
+ <title>REFERENCE</title>
+ <para>
+ 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.
+ </para>
+ </refsect1>
+
+
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>The homepage of POA is <ulink url="http://www.bioinformatics.ucla.edu/poa">http://www.bioinformatics.ucla.edu/poa</ulink>
+ </para>
+ </refsect1>
+
+ <refsect1>
+ <title>COPYRIGHTS</title>
+
+ <para>Copyright (C) 2001, 2006 Christopher Lee <email>leec@mbi.ucla.edu</email>. 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.</para>
+
+ <para>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.
+ </para>
+
+ <para>
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+ </para>
+
+ </refsect1>
+</refentry>
+
--- poa-2.0+20060928.orig/debian/control
+++ poa-2.0+20060928/debian/control
@@ -0,0 +1,30 @@
+Source: poa
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <charles-debian-nospam@plessy.org>,
+ David Paleino <d.paleino@gmail.com>,
+ Andreas Tille <tille@debian.org>
+Build-Depends: debhelper (>= 5)
+Standards-Version: 3.7.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/poa/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/poa/trunk/
+Homepage: http://www.bioinformatics.ucla.edu/poa
+
+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. POA is published in Bioinformatics. 2004 Jul
+ 10;20(10):1546-56.
![[patchlogo]](http://patch-tracker.debian.org/static/img/swirlpatch.png)