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<?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 "February 17, 2007">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>charles-debian-nospam@plessy.org</email>">
<!ENTITY dhusername "Charles Plessy">
<!ENTITY dhucpackage "<refentrytitle>KALIGN</refentrytitle>">
<!ENTITY dhpackage "kalign">
<!ENTITY dhrelease "2.03">
<!ENTITY dhtitle "Kalign User Manual">
<!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 same terms as kalign itself. -->
<refentry>
<refentryinfo>
<title>&dhtitle;</title>
<productname>&dhpackage;</productname>
<releaseinfo role="version">&dhrelease;</releaseinfo>
<date>&dhdate;</date>
<authorgroup>
<author>
<firstname>Timo</firstname>
<surname>Lassmann</surname>
<contrib>Upstream author of kalign.</contrib>
<address>
<email>timolassmann@gmail.com</email>
</address>
</author>
<author>
&dhfirstname;
&dhsurname;
<contrib>Wrote the manpage.</contrib>
<address>&dhemail;</address>
</author>
</authorgroup>
<copyright>
<year>2004</year>
<year>2005</year>
<year>2006</year>
<holder>Timo Lassmann</holder>
</copyright>
<legalnotice>
<para>
Kalign 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 same terms as kalign itself.
</para>
<para>
On Debian systems, the complete text of the GNU General Public License can be found in <filename>/usr/share/common-licenses/GPL</filename>.
</para>
</legalnotice>
</refentryinfo>
<refmeta>
&dhucpackage;
&dhsection;
</refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
<refpurpose>performs multiple alignment of biological sequences.</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg>
<replaceable>infile.fasta</replaceable>
</arg>
<arg choice="opt">
<replaceable>outfile.fasta</replaceable>
</arg>
<arg choice="opt">Options</arg>
</cmdsynopsis>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg> -i
<replaceable>infile.fasta</replaceable>
</arg>
<arg choice="opt"> -o
<replaceable>outfile.fasta</replaceable>
</arg>
<arg choice="opt">Options</arg>
</cmdsynopsis>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg> <
<replaceable>infile.fasta</replaceable>
</arg>
<arg choice="opt"> >
<replaceable>outfile.fasta</replaceable>
</arg>
<arg choice="opt">Options</arg>
</cmdsynopsis>
</refsynopsisdiv>
<refsect1>
<title>DESCRIPTION</title>
<para><command>Kalign</command> is a command line tool to perform multiple alignment of biological sequences. It employs the Wu-Manber string-matching algorithm, to improve both the accuracy and speed of the alignment. It uses global, progressive alignment approach, enriched by employing an approximate string-matching algorithm to calculate sequence distances and by incorporating local matches into the otherwise global alignment. In comparisons made by its authors, Kalign was about 10 times faster than ClustalW and, depending on the alignment size, up to 50 times faster than popular iterative methods.</para>
</refsect1>
<refsect1>
<title>OPTIONS</title>
<variablelist>
<varlistentry>
<term>
<option>-s</option>
<option>-gpo</option>
<option>-gapopen</option>
<option>-gap_open</option>
<parameter>x</parameter>
</term>
<listitem>
<para>Gap open penalty<!-- (default 6.0)-->.</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
<option>-e</option>
<option>-gpe</option>
<option>-gap_ext</option>
<option>-gapextension</option>
<parameter>x</parameter>
</term>
<listitem>
<para>Gap extension penalty.</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
<option>-t</option>
<option>-tgpe</option>
<option>-terminal_gap_extension_penalty</option>
<parameter>x</parameter>
</term>
<listitem><para>Terminal gap penalties.</para></listitem>
</varlistentry>
<varlistentry>
<term>
<option>-m</option>
<option>-bonus</option>
<option>-matrix_bonus</option>
<parameter>x</parameter>
</term>
<listitem>
<para>A constant added to the substitution matrix.</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
<option>-c</option>
<option>-sort</option>
<parameter><input, tree, gaps.></parameter>
</term>
<listitem>
<para>The order in which the sequences appear in the output alignment.</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
<option>-g</option>
<option>-feature</option>
</term>
<listitem>
<para>
Selects feature mode and specifies which features are to be used: e.g. all, maxplp, STRUCT, PFAM-A....
</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
<option>-d</option>
<option>-distance</option>
<parameter><wu, pair></parameter>
</term>
<listitem><para>Distance method</para></listitem>
</varlistentry>
<varlistentry>
<term>
<option>-b</option>
<option>-tree</option>
<option>-guide-tree</option>
<parameter><nj, upgma></parameter>
</term>
<listitem>
<para>Guide tree method.</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
<option>-z</option>
<option>-zcutoff</option>
</term>
<listitem>
<para>
Parameter used in the wu-manber based distance calculation.
</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
<option>-i</option>
<option>-in</option>
<option>-input</option>
</term>
<listitem>
<para>Name of the input file.</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
<option>-o</option>
<option>-out</option>
<option>-output</option>
</term>
<listitem>
<para>Name of the output file.</para>
</listitem>
</varlistentry>
<!-- <varlistentry>
<term><option>-p</option>
<option>-points</option>
</term>
<listitem>
<para>Wu-Manber algorithm used in both distance calculation and dynamic programming.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-w</option>
</term>
<listitem>
<para>Wu-Manber algorithm will not be used at all.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-f</option>
<option>-fast</option>
</term>
<listitem>
<para>Fast heuristic alignment ( recommended for >500 sequences)</para>
</listitem>
</varlistentry>
-->
<varlistentry>
<term>
<option>-f</option>
<option>-format</option>
<parameter><fasta, msf, aln, clu, macsim></parameter>
</term>
<listitem>
<para>The output format.</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
<option>-q</option>
<option>-quiet</option>
</term>
<listitem>
<para>Print nothing to STDERR. Read nothing from STDIN.</para>
</listitem>
</varlistentry>
</variablelist>
<!-- <para> In default mode Kalign will use the Wu-Manber algorithm for distance calculation only. (recommended for < 500 sequences)</para>-->
</refsect1>
<refsect1>
<title>REFERENCE</title>
<para>
Please cite Timo Lassmann and Erik L.L. Sonnhammer (2005) Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6:298
</para>
</refsect1>
</refentry>
|
