[med-svn] r4057 - trunk/packages/mafft/trunk/debian
Andreas Tille
tille at alioth.debian.org
Mon Sep 28 11:26:12 UTC 2009
Author: tille
Date: 2009-09-28 11:26:12 +0000 (Mon, 28 Sep 2009)
New Revision: 4057
Added:
trunk/packages/mafft/trunk/debian/docs
trunk/packages/mafft/trunk/debian/manpages
Removed:
trunk/packages/mafft/trunk/debian/mafft-homologs.1
trunk/packages/mafft/trunk/debian/mafft-homologs.1.xml
trunk/packages/mafft/trunk/debian/mafft.1
trunk/packages/mafft/trunk/debian/mafft.1.xml
Modified:
trunk/packages/mafft/trunk/debian/links
trunk/packages/mafft/trunk/debian/rules
Log:
Manpages are now included upstream, slightly changed debhelper inputs to keep debian/rules cleaner
Added: trunk/packages/mafft/trunk/debian/docs
===================================================================
--- trunk/packages/mafft/trunk/debian/docs (rev 0)
+++ trunk/packages/mafft/trunk/debian/docs 2009-09-28 11:26:12 UTC (rev 4057)
@@ -0,0 +1 @@
+test
Modified: trunk/packages/mafft/trunk/debian/links
===================================================================
--- trunk/packages/mafft/trunk/debian/links 2009-09-28 11:22:36 UTC (rev 4056)
+++ trunk/packages/mafft/trunk/debian/links 2009-09-28 11:26:12 UTC (rev 4057)
@@ -1,14 +1,13 @@
-usr/share/man/man1/mafft.1 /usr/share/man/man1/mafft-linsi.1
-usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-ginsi.1
-usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-einsi.1
-usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-fftnsi.1
-usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-fftns.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-linsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-ginsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-einsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-fftnsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-fftns.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/linsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/ginsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/einsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/fftnsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/fftns.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-profile.1
-usr/share/man/man1/mafft.1 usr/share/man/man1/linsi.1
-usr/share/man/man1/mafft.1 usr/share/man/man1/ginsi.1
-usr/share/man/man1/mafft.1 usr/share/man/man1/einsi.1
-usr/share/man/man1/mafft.1 usr/share/man/man1/fftnsi.1
-usr/share/man/man1/mafft.1 usr/share/man/man1/fftns.1
-
-usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-profile.1
-
+usr/lib/mafft/bin/mafft-homologs.rb usr/bin/mafft-homologs
Deleted: trunk/packages/mafft/trunk/debian/mafft-homologs.1
===================================================================
--- trunk/packages/mafft/trunk/debian/mafft-homologs.1 2009-09-28 11:22:36 UTC (rev 4056)
+++ trunk/packages/mafft/trunk/debian/mafft-homologs.1 2009-09-28 11:26:12 UTC (rev 4057)
@@ -1,112 +0,0 @@
-.\" Title: MAFFT-HOMOLOGS
-.\" Author: Kazutaka Katoh <katoh_at_bioreg.kyushu-u.ac.jp.>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 2008-09-01
-.\" Manual: Mafft Manual
-.\" Source: mafft-homologs 2.1
-.\"
-.TH "MAFFT\-HOMOLOGS" "1" "2008\-09\-01" "mafft-homologs 2.1" "Mafft Manual"
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.SH "NAME"
-mafft-homologs \- aligns sequences together with homologues automatically collected from SwissProt via NCBI BLAST
-.SH "SYNOPSIS"
-.HP 15
-\fBmafft\-homologs\fR [\fBoptions\fR] \fIinput\fR [>\ \fIoutput\fR]
-.SH "DESCRIPTION"
-.PP
-The accuracy of an alignment of a few distantly related sequences is considerably improved when being aligned together with their close homologs\&. The reason for the improvement is probably the same as that for PSI\-BLAST\&. That is, the positions of highly conserved residues, those with many gaps and other additional information is brought by close homologs\&. According to Katoh et al\&. (2005), the improvement by adding close homologs is 10% or so, which is comparable to the improvement by incorporating structural information of a pair of sequences\&. Mafft\-homologs in a mafft server works like this:
-.sp
-.RS 4
-\h'-04' 1.\h'+02'Collect a number (50 by default) of close homologs (E=1e\-10 by default) of the input sequences\&.
-.RE
-.sp
-.RS 4
-\h'-04' 2.\h'+02'Align the input sequences and homologs all together using the L\-INS\-i strategy\&.
-.RE
-.sp
-.RS 4
-\h'-04' 3.\h'+02'Remove the homologs\&.
-.RE
-.SH "OPTIONS"
-.PP
-\fB\-a\fR \fI\fIn\fR\fR
-.RS 4
-The number of collected sequences (default: 50)\&.
-.RE
-.PP
-\fB\-e\fR \fI\fIn\fR\fR
-.RS 4
-Threshold value (default: 1e\-10)\&.
-.RE
-.PP
-\fB\-o\fR \fI\fIxxx\fR\fR
-.RS 4
-options for mafft (default: " \-\-op 1\&.53 \-\-ep 0\&.123 \-\-maxiterate 1000")\&.
-.RE
-.PP
-\fB\-l\fR
-.RS 4
-Locally carries out blast searches instead of NCBI blast (requires locally installed blast and a database)\&.
-.RE
-.PP
-\fB\-f\fR
-.RS 4
-Outputs collected homologues also (default: off)\&.
-.RE
-.PP
-\fB\-w\fR
-.RS 4
-entire sequences are subjected to BLAST search (default: well\-aligned region only)
-.RE
-.SH "REQUIREMENTS"
-.PP
-Mafft\-homologs requires a version of mafft higher than 5\&.58\&.
-.SH "REFERENCES"
-.PP
-Katoh, Kuma, Toh and Miyata (Nucleic Acids Res\&. 33:511\-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment\&.
-.SH "SEE ALSO"
-.PP
-
-\fBmafft\fR(1)
-.SH "DIVERGENCE FROM UPSTREAM"
-.PP
-\fBmafft\-homologs\fR
-has been patched to enhance the security of the temporary files it creates\&. You can consult the patch in the Debian source package\&. It has been reviewed and amended by Kazutaka Katoh, the upstream author of MAFFT\&.
-.SH "AUTHORS"
-.PP
-\fBKazutaka Katoh\fR <\&katoh_at_bioreg\&.kyushu\-u\&.ac\&.jp\&.\&>
-.sp -1n
-.IP "" 4
-Wrote Mafft\&.
-.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\&.org\&>
-.sp -1n
-.IP "" 4
-Wrote this manpage in DocBook XML for the Debian distribution, using Mafft\'s homepage as a template\&.
-.SH "COPYRIGHT"
-Copyright \(co 2002, 2003, 2004, 2005, 2006, 2007 Kazutaka Katoh (mafft)
-.br
-Copyright \(co 2007 Charles Plessy (this manpage)
-.br
-.PP
-Mafft and its manpage are offered under the following conditions:
-.PP
-Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-.sp
-.RS 4
-\h'-04' 1.\h'+02'Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer\&.
-.RE
-.sp
-.RS 4
-\h'-04' 2.\h'+02'Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution\&.
-.RE
-.sp
-.RS 4
-\h'-04' 3.\h'+02'The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission\&.
-.RE
-.PP
-THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED\&. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE\&.
-.sp
Deleted: trunk/packages/mafft/trunk/debian/mafft-homologs.1.xml
===================================================================
--- trunk/packages/mafft/trunk/debian/mafft-homologs.1.xml 2009-09-28 11:22:36 UTC (rev 4056)
+++ trunk/packages/mafft/trunk/debian/mafft-homologs.1.xml 2009-09-28 11:26:12 UTC (rev 4057)
@@ -1,201 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<?xml-stylesheet type="text/xsl"
- href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
-<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
- "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
-
-<!-- This manpage is based in the expample from the docbook-xsl
- package version 1.72.0.dfsg.1-1 from Debian.-->
-
- <!ENTITY dhfirstname "Charles">
- <!ENTITY dhsurname "Plessy">
- <!ENTITY dhemail "charles-debian-nospam at plessy.org">
- <!ENTITY dhusername "&dhfirstname; &dhsurname;">
- <!ENTITY dhrelease "2.1">
- <!ENTITY dhdate "2008-09-01">
- <!ENTITY dhtitle "Mafft Manual">
- <!ENTITY dhucpackage "MAFFT-HOMOLOGS">
- <!ENTITY dhpackage "mafft-homologs">
- <!ENTITY dhproduct "&dhpackage;">
- <!ENTITY dhsection "1">
-]>
-
-<refentry>
- <refentryinfo>
- <title>&dhtitle;</title>
- <productname>&dhpackage;</productname>
- <releaseinfo role="version">&dhrelease;</releaseinfo>
- <date>&dhdate;</date>
- <authorgroup>
- <author>
- <firstname>Kazutaka</firstname>
- <surname>Katoh</surname>
- <contrib>Wrote Mafft.</contrib>
- <address>
- <email>katoh_at_bioreg.kyushu-u.ac.jp.</email>
- </address>
- </author>
- <author>
- <firstname>&dhfirstname;</firstname>
- <surname>&dhsurname;</surname>
- <contrib>Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template.</contrib>
- <address>
- <email>&dhemail;</email>
- </address>
- </author>
- </authorgroup>
- <copyright>
- <year>2002</year>
- <year>2003</year>
- <year>2004</year>
- <year>2005</year>
- <year>2006</year>
- <year>2007</year>
- <holder>Kazutaka Katoh (mafft)</holder>
- </copyright>
- <copyright>
- <year>2007</year>
- <holder>&dhusername; (this manpage)</holder>
- </copyright>
- <legalnotice>
- <para>Mafft and its manpage are offered under the following conditions:</para>
- <para>Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:</para>
- <orderedlist>
- <listitem>
- <para>Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.</para>
- </listitem>
- <listitem>
- <para>Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.</para>
- </listitem>
- <listitem>
- <para>The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission.</para>
- </listitem>
- </orderedlist>
- <para>THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</para>
- </legalnotice>
- </refentryinfo>
-
- <refmeta>
- <refentrytitle>&dhucpackage;</refentrytitle>
- <manvolnum>&dhsection;</manvolnum>
- </refmeta>
-
- <refnamediv>
- <refname>&dhpackage;</refname>
- <refpurpose>aligns sequences together with homologues automatically collected from SwissProt via NCBI BLAST</refpurpose>
- </refnamediv>
-
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <arg choice="opt"><option>options</option></arg>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
- </refsynopsisdiv>
-
- <refsect1 id="description">
- <title>DESCRIPTION</title>
- <para>The accuracy of an alignment of a few distantly related sequences is considerably improved when being aligned together with their close homologs. The reason for the improvement is probably the same as that for PSI-BLAST. That is, the positions of highly conserved residues, those with many gaps and other additional information is brought by close homologs. According to Katoh et al. (2005), the improvement by adding close homologs is 10% or so, which is comparable to the improvement by incorporating structural information of a pair of sequences. Mafft-homologs in a mafft server works like this:</para>
- <orderedlist>
- <listitem>
- <para>Collect a number (50 by default) of close homologs (E=1e-10 by default) of the input sequences.</para>
- </listitem>
-
- <listitem>
- <para>Align the input sequences and homologs all together using the L-INS-i strategy.</para>
- </listitem>
-
- <listitem>
- <para>Remove the homologs.</para>
- </listitem>
- </orderedlist>
- </refsect1>
-
- <refsect1 id="options">
- <title>OPTIONS</title>
- <variablelist>
- <!-- Use the variablelist.term.separator and the
- variablelist.term.break.after parameters to
- control the term elements. -->
- <varlistentry>
- <term>
- <option>-a</option>
- <varname><replaceable>n</replaceable></varname>
- </term>
- <listitem>
- <para>The number of collected sequences (default: 50).</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-e</option>
- <varname><replaceable>n</replaceable></varname>
- </term>
- <listitem>
- <para>Threshold value (default: 1e-10).</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-o</option>
- <varname><replaceable>xxx</replaceable></varname>
- </term>
- <listitem>
- <para>options for mafft (default: " --op 1.53 --ep 0.123 --maxiterate 1000").</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-l</option></term>
- <listitem>
- <para>Locally carries out blast searches instead of NCBI blast (requires locally installed blast and a database).</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-f</option></term>
- <listitem>
- <para>Outputs collected homologues also (default: off).</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-w</option></term>
- <listitem>
- <para>entire sequences are subjected to BLAST search (default: well-aligned region only)</para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
-
- <refsect1 id="files">
- <title>REQUIREMENTS</title>
- <para>Mafft-homologs requires a version of mafft higher than 5.58.</para>
- </refsect1>
-
- <refsect1 id="references">
- <title>REFERENCES</title>
- <para>Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment.</para>
- </refsect1>
-
- <refsect1 id="see_also">
- <title>SEE ALSO</title>
- <!-- In alpabetical order. -->
- <para>
- <citerefentry>
- <refentrytitle>mafft</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry>
- </para>
- </refsect1>
- <refsect1>
- <title>DIVERGENCE FROM UPSTREAM</title>
- <para><command>mafft-homologs</command> has been patched to enhance the
- security of the temporary files it creates. You can consult the patch in
- the Debian source package. It has been reviewed and amended by Kazutaka
- Katoh, the upstream author of MAFFT.</para>
- </refsect1>
-</refentry>
Deleted: trunk/packages/mafft/trunk/debian/mafft.1
===================================================================
--- trunk/packages/mafft/trunk/debian/mafft.1 2009-09-28 11:22:36 UTC (rev 4056)
+++ trunk/packages/mafft/trunk/debian/mafft.1 2009-09-28 11:26:12 UTC (rev 4057)
@@ -1,370 +0,0 @@
-.\" Title: MAFFT
-.\" Author: Kazutaka Katoh <katoh_at_bioreg.kyushu-u.ac.jp.>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 2008-09-01
-.\" Manual: Mafft Manual
-.\" Source: mafft 6.240
-.\"
-.TH "MAFFT" "1" "2008\-09\-01" "mafft 6.240" "Mafft Manual"
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.SH "NAME"
-mafft \- Multiple alignment program for amino acid or nucleotide sequences
-.SH "SYNOPSIS"
-.HP 6
-\fBmafft\fR [\fBoptions\fR] \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBlinsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBginsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBeinsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 7
-\fBfftnsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBfftns\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 14
-\fBmafft\-profile\fR \fIgroup1\fR \fIgroup2\fR [>\ \fIoutput\fR]
-.SH "DESCRIPTION"
-.PP
-\fBMAFFT\fR
-is a multiple sequence alignment program for unix\-like operating systems\&. It offers a range of multiple alignment methods\&.
-.SS "Accuracy\-oriented methods:"
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'L\-INS\-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
-.HP 6
-\fBmafft\fR \fB\-\-localpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBlinsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'G\-INS\-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
-.HP 6
-\fBmafft\fR \fB\-\-globalpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBginsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'E\-INS\-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
-.HP 6
-\fBmafft\fR \fB\-\-ep\fR\ \fI0\fR \fB\-\-genafpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBeinsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.br
-
-For E\-INS\-i, the
-\fB\-\-ep\fR
-\fI0\fR
-option is recommended to allow large gaps\&.
-.RE
-.SS "Speed\-oriented methods:"
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'FFT\-NS\-i (iterative refinement method; two cycles only):
-.HP 6
-\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI2\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 7
-\fBfftnsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'FFT\-NS\-i (iterative refinement method; max\&. 1000 iterations):
-.HP 6
-\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'FFT\-NS\-2 (fast; progressive method):
-.HP 6
-\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI0\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBfftns\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'FFT\-NS\-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):
-.HP 6
-\fBmafft\fR \fB\-\-retree\fR\ \fI1\fR \fB\-\-maxiterate\fR\ \fI0\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'NW\-NS\-PartTree\-1 (recommended for ?50,000 sequences; progressive method with the PartTree algorithm):
-.HP 6
-\fBmafft\fR \fB\-\-retree\fR\ \fI1\fR \fB\-\-maxiterate\fR\ \fI0\fR \fB\-\-parttree\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.SS "Group\-to\-group alignments"
-.HP 14
-\fBmafft\-profile\fR \fIgroup1\fR \fIgroup2\fR [>\ \fIoutput\fR]
-.PP
-or:
-.HP 6
-\fBmafft\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fB\-\-seed\fR\ \fIgroup1\fR \fB\-\-seed\fR\ \fIgroup2\fR /dev/null [>\ \fIoutput\fR]
-.SH "OPTIONS"
-.PP
-\fB\-\-auto\fR
-.RS 4
-.RE
-.PP
-\fB\-\-clustalout\fR
-.RS 4
-.RE
-.PP
-\fB\-\-reorder\fR
-.RS 4
-.RE
-.PP
-\fB\-\-inputorder\fR
-.RS 4
-.RE
-.PP
-\fB\-\-algq\fR
-.RS 4
-.RE
-.PP
-\fB\-\-groupsize\fR
-.RS 4
-.RE
-.PP
-\fB\-\-partsize\fR
-.RS 4
-.RE
-.PP
-\fB\-\-parttree\fR
-.RS 4
-.RE
-.PP
-\fB\-\-dpparttree\fR
-.RS 4
-.RE
-.PP
-\fB\-\-fastaparttree\fR
-.RS 4
-.RE
-.PP
-\fB\-\-treeout\fR
-.RS 4
-.RE
-.PP
-\fB\-\-fastswpair\fR
-.RS 4
-.RE
-.PP
-\fB\-\-fastapair\fR
-.RS 4
-.RE
-.PP
-\fB\-\-noscore\fR
-.RS 4
-.RE
-.PP
-\fB\-\-6merpair\fR
-.RS 4
-.RE
-.PP
-\fB\-\-blastpair\fR
-.RS 4
-.RE
-.PP
-\fB\-\-globalpair\fR
-.RS 4
-.RE
-.PP
-\fB\-\-localpair\fR
-.RS 4
-.RE
-.PP
-\fB\-\-genafpair\fR
-.RS 4
-.RE
-.PP
-\fB\-\-memsave\fR
-.RS 4
-.RE
-.PP
-\fB\-\-nuc\fR
-.RS 4
-.RE
-.PP
-\fB\-\-amino\fR
-.RS 4
-.RE
-.PP
-\fB\-\-fft\fR
-.RS 4
-.RE
-.PP
-\fB\-\-nofft\fR
-.RS 4
-.RE
-.PP
-\fB\-\-quiet\fR
-.RS 4
-.RE
-.PP
-\fB\-\-coreext\fR
-.RS 4
-.RE
-.PP
-\fB\-\-core\fR
-.RS 4
-.RE
-.PP
-\fB\-\-maxiterate\fR
-.RS 4
-.RE
-.PP
-\fB\-\-retree\fR
-.RS 4
-.RE
-.PP
-\fB\-\-aamatrix\fR
-.RS 4
-.RE
-.PP
-\fB\-\-fmodel\fR
-.RS 4
-.RE
-.PP
-\fB\-\-jtt\fR
-.RS 4
-.RE
-.PP
-\fB\-\-tm\fR
-.RS 4
-.RE
-.PP
-\fB\-\-bl\fR
-.RS 4
-.RE
-.PP
-\fB\-\-weighti\fR
-.RS 4
-.RE
-.PP
-\fB\-\-op\fR
-.RS 4
-.RE
-.PP
-\fB\-\-ep\fR
-.RS 4
-.RE
-.PP
-\fB\-\-lop\fR
-.RS 4
-.RE
-.PP
-\fB\-\-LOP\fR
-.RS 4
-.RE
-.PP
-\fB\-\-lep\fR
-.RS 4
-.RE
-.PP
-\fB\-\-lexp\fR
-.RS 4
-.RE
-.PP
-\fB\-\-LEXP\fR
-.RS 4
-.RE
-.PP
-\fB\-\-corethr\fR
-.RS 4
-.RE
-.PP
-\fB\-\-corewin\fR
-.RS 4
-.RE
-.PP
-\fB\-\-seed\fR
-.RS 4
-.RE
-.SH "FILES"
-.PP
-Mafft stores the input sequences and other files in a temporary directory, which by default is located in
-\fI/tmp\fR\&.
-.SH "ENVIONMENT"
-.PP
-\fBMAFFT_BINARIES\fR
-.RS 4
-Indicates the location of the binary files used by mafft\&. By default, they are searched in
-\fI/usr/local/lib/mafft\fR, but on Debian systems, they are searched in
-\fI/usr/lib/mafft\fR\&.
-.RE
-.PP
-\fBFASTA_4_MAFFT\fR
-.RS 4
-This variable can be set to indicate to mafft the location to the fasta34 program if it is not in the PATH\&.
-.RE
-.SH "SEE ALSO"
-.PP
-
-\fBmafft-homologs\fR(1)
-.SH "REFERENCES"
-.SS "In English"
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'Katoh and Toh (Bioinformatics 23:372\-374, 2007) PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences (describes the PartTree algorithm)\&.
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'Katoh, Kuma, Toh and Miyata (Nucleic Acids Res\&. 33:511\-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment (describes [ancestral versions of] the G\-INS\-i, L\-INS\-i and E\-INS\-i strategies)
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'Katoh, Misawa, Kuma and Miyata (Nucleic Acids Res\&. 30:3059\-3066, 2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform (describes the FFT\-NS\-1, FFT\-NS\-2 and FFT\-NS\-i strategies)
-.RE
-.SS "In Japanese"
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'Katoh and Misawa (???? 46:312\-317, 2006) Multiple Sequence Alignments: the Next Generation
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'Katoh and Kuma (????? 44:102\-108, 2006) Jissen\-teki Multiple Alignment
-.RE
-.SH "DIVERGENCE FROM UPSTREAM"
-.PP
-\fBmafft\-homologs\fR
-has been patched to enhance the security of the temporary files it creates\&. You can consult the patch in the Debian source package\&. It has been reviewed and amended by Kazutaka Katoh, the upstream author of MAFFT\&.
-.SH "AUTHORS"
-.PP
-\fBKazutaka Katoh\fR <\&katoh_at_bioreg\&.kyushu\-u\&.ac\&.jp\&.\&>
-.sp -1n
-.IP "" 4
-Wrote Mafft\&.
-.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\&.org\&>
-.sp -1n
-.IP "" 4
-Wrote this manpage in DocBook XML for the Debian distribution, using Mafft\'s homepage as a template\&.
-.SH "COPYRIGHT"
-Copyright \(co 2002, 2003, 2004, 2005, 2006, 2007 Kazutaka Katoh (mafft)
-.br
-Copyright \(co 2007 Charles Plessy (this manpage)
-.br
-.PP
-Mafft and its manpage are offered under the following conditions:
-.PP
-Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-.sp
-.RS 4
-\h'-04' 1.\h'+02'Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer\&.
-.RE
-.sp
-.RS 4
-\h'-04' 2.\h'+02'Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution\&.
-.RE
-.sp
-.RS 4
-\h'-04' 3.\h'+02'The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission\&.
-.RE
-.PP
-THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED\&. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE\&.
-.sp
Deleted: trunk/packages/mafft/trunk/debian/mafft.1.xml
===================================================================
--- trunk/packages/mafft/trunk/debian/mafft.1.xml 2009-09-28 11:22:36 UTC (rev 4056)
+++ trunk/packages/mafft/trunk/debian/mafft.1.xml 2009-09-28 11:26:12 UTC (rev 4057)
@@ -1,749 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<?xml-stylesheet type="text/xsl"
- href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
-<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
- "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
-
-<!-- This manpage is based in the expample from the docbook-xsl
- package version 1.72.0.dfsg.1-1 from Debian.-->
-
- <!ENTITY dhfirstname "Charles">
- <!ENTITY dhsurname "Plessy">
- <!ENTITY dhemail "charles-debian-nospam at plessy.org">
- <!ENTITY dhusername "&dhfirstname; &dhsurname;">
- <!ENTITY dhrelease "6.240">
- <!ENTITY dhdate "2008-09-01">
- <!ENTITY dhtitle "Mafft Manual">
- <!ENTITY dhucpackage "MAFFT">
- <!ENTITY dhpackage "mafft">
- <!ENTITY dhproduct "&dhpackage;">
- <!ENTITY dhsection "1">
-]>
-
-<refentry>
- <refentryinfo>
- <title>&dhtitle;</title>
- <productname>&dhpackage;</productname>
- <releaseinfo role="version">&dhrelease;</releaseinfo>
- <date>&dhdate;</date>
- <authorgroup>
- <author>
- <firstname>Kazutaka</firstname>
- <surname>Katoh</surname>
- <contrib>Wrote Mafft.</contrib>
- <address>
- <email>katoh_at_bioreg.kyushu-u.ac.jp.</email>
- </address>
- </author>
- <author>
- <firstname>&dhfirstname;</firstname>
- <surname>&dhsurname;</surname>
- <contrib>Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template.</contrib>
- <address>
- <email>&dhemail;</email>
- </address>
- </author>
- </authorgroup>
- <copyright>
- <year>2002</year>
- <year>2003</year>
- <year>2004</year>
- <year>2005</year>
- <year>2006</year>
- <year>2007</year>
- <holder>Kazutaka Katoh (mafft)</holder>
- </copyright>
- <copyright>
- <year>2007</year>
- <holder>&dhusername; (this manpage)</holder>
- </copyright>
- <legalnotice>
- <para>Mafft and its manpage are offered under the following conditions:</para>
- <para>Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:</para>
- <orderedlist>
- <listitem>
- <para>Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.</para>
- </listitem>
- <listitem>
- <para>Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.</para>
- </listitem>
- <listitem>
- <para>The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission.</para>
- </listitem>
- </orderedlist>
- <para>THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</para>
- </legalnotice>
- </refentryinfo>
-
- <refmeta>
- <refentrytitle>&dhucpackage;</refentrytitle>
- <manvolnum>&dhsection;</manvolnum>
- </refmeta>
-
- <refnamediv>
- <refname>&dhpackage;</refname>
- <refpurpose>Multiple alignment program for amino acid or nucleotide sequences</refpurpose>
- </refnamediv>
-
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <arg choice="opt"><option>options</option></arg>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
-
- <cmdsynopsis>
- <command>linsi</command>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
-
- <cmdsynopsis>
- <command>ginsi</command>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
-
- <cmdsynopsis>
- <command>einsi</command>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
-
- <cmdsynopsis>
- <command>fftnsi</command>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
-
- <cmdsynopsis>
- <command>fftns</command>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
-
- <cmdsynopsis>
- <command>mafft-profile</command>
- <arg choice="plain"><replaceable>group1</replaceable></arg>
- <arg choice="plain"><replaceable>group2</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
- </refsynopsisdiv>
-
- <refsect1 id="description">
- <title>DESCRIPTION</title>
-
- <para><command>&dhucpackage;</command> is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods.</para>
-
- <refsect2>
- <title>Accuracy-oriented methods:</title>
- <itemizedlist>
- <listitem>
- <para>L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):</para>
-
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <arg choice="plain"><option>--localpair</option></arg>
- <arg choice="plain">
- <option>--maxiterate</option>
- <replaceable>1000</replaceable>
- </arg>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
-
- <cmdsynopsis>
- <command>linsi</command>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
- </listitem>
-
- <listitem>
- <para>G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):</para>
-
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <arg choice="plain"><option>--globalpair</option></arg>
- <arg choice="plain">
- <option>--maxiterate</option>
- <replaceable>1000</replaceable>
- </arg>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
-
- <cmdsynopsis>
- <command>ginsi</command>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
- </listitem>
-
- <listitem>
- <para>E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):</para>
-
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <arg choice="plain">
- <option>--ep</option>
- <replaceable>0</replaceable>
- </arg>
- <arg choice="plain"><option>--genafpair</option></arg>
- <arg choice="plain">
- <option>--maxiterate</option>
- <replaceable>1000</replaceable>
- </arg>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
-
- <cmdsynopsis>
- <command>einsi</command>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- <sbr/>
- </cmdsynopsis>
-
- <para>For E-INS-i, the <option>--ep</option> <replaceable>0</replaceable> option is recommended to allow large gaps.</para>
- </listitem>
- </itemizedlist>
- </refsect2>
-
- <refsect2>
- <title>Speed-oriented methods:</title>
- <itemizedlist>
- <listitem>
- <para>FFT-NS-i (iterative refinement method; two cycles only):</para>
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <arg choice="plain">
- <option>--retree</option>
- <replaceable>2</replaceable>
- </arg>
- <arg choice="plain">
- <option>--maxiterate</option>
- <replaceable>2</replaceable>
- </arg>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
-
- <cmdsynopsis>
- <command>fftnsi</command>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
- </listitem>
-
- <listitem>
- <para>FFT-NS-i (iterative refinement method; max. 1000 iterations): </para>
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <arg choice="plain">
- <option>--retree</option>
- <replaceable>2</replaceable>
- </arg>
- <arg choice="plain">
- <option>--maxiterate</option>
- <replaceable>1000</replaceable>
- </arg>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
- </listitem>
-
- <listitem>
- <para>FFT-NS-2 (fast; progressive method):</para>
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <arg choice="plain">
- <option>--retree</option>
- <replaceable>2</replaceable>
- </arg>
- <arg choice="plain">
- <option>--maxiterate</option>
- <replaceable>0</replaceable>
- </arg>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
-
- <cmdsynopsis>
- <command>fftns</command>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
- </listitem>
-
- <listitem>
- <para>FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):</para>
-
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <arg choice="plain">
- <option>--retree</option>
- <replaceable>1</replaceable>
- </arg>
- <arg choice="plain">
- <option>--maxiterate</option>
- <replaceable>0</replaceable>
- </arg>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
- </listitem>
-
- <listitem>
- <para>NW-NS-PartTree-1 (recommended for ?50,000 sequences; progressive method with the PartTree algorithm):</para>
-
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <arg choice="plain">
- <option>--retree</option>
- <replaceable>1</replaceable>
- </arg>
- <arg choice="plain">
- <option>--maxiterate</option>
- <replaceable>0</replaceable>
- </arg>
- <arg choice="plain"><option>--parttree</option></arg>
- <arg choice="plain"><replaceable>input</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
- </listitem>
- </itemizedlist>
- </refsect2>
-
- <refsect2>
- <title>Group-to-group alignments</title>
-
- <cmdsynopsis>
- <command>mafft-profile</command>
- <arg choice="plain"><replaceable>group1</replaceable></arg>
- <arg choice="plain"><replaceable>group2</replaceable></arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
-
- <para>or:</para>
-
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <arg choice="plain">
- <option>--maxiterate</option>
- <replaceable>1000</replaceable>
- </arg>
- <arg choice="plain">
- <option>--seed</option>
- <replaceable>group1</replaceable>
- </arg>
- <arg choice="plain">
- <option>--seed</option>
- <replaceable>group2</replaceable>
- </arg>
- <arg choice="plain">/dev/null</arg>
- <arg choice="opt">> <replaceable>output</replaceable></arg>
- </cmdsynopsis>
- </refsect2>
- </refsect1>
-
- <refsect1 id="options">
- <title>OPTIONS</title>
- <variablelist>
- <!-- Use the variablelist.term.separator and the
- variablelist.term.break.after parameters to
- control the term elements. -->
- <varlistentry>
- <term><option>--auto</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--clustalout</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--reorder</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--inputorder</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--algq</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--groupsize</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--partsize</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--parttree</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--dpparttree</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--fastaparttree</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--treeout</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--fastswpair</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--fastapair</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--noscore</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--6merpair</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--blastpair</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--globalpair</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--localpair</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--genafpair</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--memsave</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--nuc</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--amino</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--fft</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--nofft</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--quiet</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--coreext</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--core</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--maxiterate</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--retree</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--aamatrix</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--fmodel</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--jtt</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--tm</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--bl</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--weighti</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--op</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--ep</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--lop</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--LOP</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--lep</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--lexp</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--LEXP</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--corethr</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--corewin</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>--seed</option></term>
- <listitem>
- <para></para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
-
- <refsect1 id="files">
- <title>FILES</title>
- <para>Mafft stores the input sequences and other files in a temporary directory, which by default is located in <filename class="directory">/tmp</filename>.</para>
- </refsect1>
-
- <refsect1 id="environment">
- <title>ENVIONMENT</title>
- <variablelist>
- <varlistentry>
- <term><envar>MAFFT_BINARIES</envar></term>
- <listitem>
- <para>Indicates the location of the binary files used by mafft. By default, they are searched in <filename class="directory">/usr/local/lib/mafft</filename>, but on Debian systems, they are searched in <filename class="directory">/usr/lib/mafft</filename>.</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><envar>FASTA_4_MAFFT</envar></term>
- <listitem>
- <para>This variable can be set to indicate to mafft the location to the fasta34 program if it is not in the PATH.</para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
-
- <refsect1 id="see_also">
- <title>SEE ALSO</title>
- <!-- In alpabetical order. -->
- <para>
- <citerefentry>
- <refentrytitle>mafft-homologs</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry>
- </para>
- </refsect1>
-
- <refsect1 id="references">
- <title>REFERENCES</title>
- <refsect2>
- <title>In English</title>
- <itemizedlist>
- <listitem>
- <para>Katoh and Toh (Bioinformatics 23:372-374, 2007) PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences (describes the PartTree algorithm).</para>
- </listitem>
-
- <listitem>
- <para>Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment (describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies)</para>
- </listitem>
-
- <listitem>
- <para>Katoh, Misawa, Kuma and Miyata (Nucleic Acids Res. 30:3059-3066, 2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform (describes the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies)</para>
- </listitem>
- </itemizedlist>
- </refsect2>
-
- <refsect2>
- <title>In Japanese</title>
- <itemizedlist>
- <listitem>
- <para>Katoh and Misawa (???? 46:312-317, 2006) Multiple Sequence Alignments: the Next Generation</para>
- </listitem>
-
- <listitem>
- <para>Katoh and Kuma (????? 44:102-108, 2006) Jissen-teki Multiple Alignment</para>
- </listitem>
- </itemizedlist>
- </refsect2>
- </refsect1>
- <refsect1>
- <title>DIVERGENCE FROM UPSTREAM</title>
- <para><command>mafft-homologs</command> has been patched to enhance the
- security of the temporary files it creates. You can consult the patch in
- the Debian source package. It has been reviewed and amended by Kazutaka
- Katoh, the upstream author of MAFFT.</para>
- </refsect1>
-</refentry>
-
Added: trunk/packages/mafft/trunk/debian/manpages
===================================================================
--- trunk/packages/mafft/trunk/debian/manpages (rev 0)
+++ trunk/packages/mafft/trunk/debian/manpages 2009-09-28 11:26:12 UTC (rev 4057)
@@ -0,0 +1 @@
+core/*.1
Modified: trunk/packages/mafft/trunk/debian/rules
===================================================================
--- trunk/packages/mafft/trunk/debian/rules 2009-09-28 11:22:36 UTC (rev 4056)
+++ trunk/packages/mafft/trunk/debian/rules 2009-09-28 11:26:12 UTC (rev 4057)
@@ -48,7 +48,8 @@
clean:
dh_testdir
dh_testroot
- [ ! -f Makefile ] || $(MAKE) -C core clean
+ [ ! -f core/Makefile ] || $(MAKE) -C core clean
+ # rm -rf binaries/*
dh_clean build-stamp
install: build-stamp test
@@ -57,7 +58,6 @@
dh_clean -k
dh_installdirs
$(MAKE) -C core PREFIX=$(CURDIR)/debian/mafft/usr/lib/mafft install
- mv core/mafft-homologs.rb debian/mafft/usr/bin/mafft-homologs
binary-indep: build install
binary-arch: build install
@@ -65,8 +65,8 @@
dh_testroot
dh_installchangelogs
dh_installdocs
- dh_install test usr/share/doc/mafft/
- dh_installman debian/mafft.1 debian/mafft-homologs.1
+ dh_install
+ dh_installman
dh_link
dh_strip
dh_compress
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