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<?xml version='1.0' encoding='ISO-8859-1'?>
<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.2//EN"
"http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd" [
<!--
Process this file with an XSLT processor: `xsltproc \
-''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
manpages/docbook.xsl manpage.dbk'. A manual page
<package>.<section> will be generated. You may view the
manual page with: nroff -man <package>.<section> | less'. A
typical entry in a Makefile or Makefile.am is:
DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
manpages/docbook.xsl
XP=xsltproc -''-nonet
manpage.1: manpage.dbk
$(XP) $(DB2MAN) $<
The xsltproc binary is found in the xsltproc package. The
XSL files are in docbook-xsl. Please remember that if you
create the nroff version in one of the debian/rules file
targets (such as build), you will need to include xsltproc
and docbook-xsl in your Build-Depends control field.
-->
<!-- Fill in your name for FIRSTNAME and SURNAME. -->
<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
<!ENTITY dhsurname "<surname>Moeller</surname>">
<!-- Please adjust the date whenever revising the manpage. -->
<!ENTITY dhdate "<date>September 19, 2004</date>">
<!-- SECTION should be 1-8, maybe w/ subsection other parameters are
allowed: see man(7), man(1). -->
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
<!ENTITY dhusername "Steffen Moeller">
<!ENTITY dhucpackage "<refentrytitle>MUSCLE</refentrytitle>">
<!ENTITY dhpackage "muscle">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
]>
<refentry>
<refentryinfo>
<address>
&dhemail;
</address>
<author>
&dhfirstname;
&dhsurname;
</author>
<copyright>
<year>2003</year>
<holder>&dhusername;</holder>
</copyright>
&dhdate;
</refentryinfo>
<refmeta>
&dhucpackage;
&dhsection;
</refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
<refpurpose>Multiple Protein Sequence Alignment</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg><option>-in <replaceable>input file (fasta)</replaceable></option></arg>
<arg><option>-out <replaceable>output file (default fasta)</replaceable></option></arg>
<arg><option>-log <replaceable>log file</replaceable></option></arg>
<arg><option>-maxiters <replaceable>n</replaceable></option></arg>
<arg><option>-maxhours <replaceable>n</replaceable></option></arg>
<arg><option>-clw</option></arg>
<arg><option>-clwstrict</option></arg>
<arg><option>-html</option></arg>
<arg><option>-msf</option></arg>
<arg><option>-quiet</option></arg>
<arg><option>-group</option></arg>
<arg><option>-stable</option></arg>
<arg><option>-version</option></arg>
<arg><option>-out <replaceable>output file</replaceable></option></arg>
</cmdsynopsis>
</refsynopsisdiv>
<refsect1>
<title>DESCRIPTION</title>
<para>This manual page documents briefly the
<command>&dhpackage;</command> command.
</para>
<para>This manual page was written for the &debian; distribution
because the original program does not have a manual page.
</para>
<para><command>&dhpackage;</command> aligns protein sequences and is considered superior and faster than clustalw.</para>
</refsect1>
<refsect1>
<title>OPTIONS</title>
<variablelist>
<varlistentry>
<term><option>-in <replaceable>input file</replaceable></option>
</term>
<listitem>
<para>Path to FASTA formatted input file
</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-out <replaceable>output file</replaceable></option>
</term>
<listitem>
<para>Path to output file, FASTA formatted by default.
</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-maxiters <replaceable>n</replaceable></option>
</term>
<listitem>
<para>Maximum number of iterations (integer, default 16)
</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-maxhours <replaceable>n</replaceable></option>
</term>
<listitem>
<para>Maximum time to iterate in hours (default no limit)
</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-clw</option>
</term>
<listitem>
<para>Write output in CLUSTALW format (default FASTA)</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-clwstrict</option>
</term>
<listitem>
<para>As -clw, with 'CLUSTAL W (1.81)' header</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-html</option>
</term>
<listitem>
<para>Write output in HTML format (default FASTA)</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-msf</option>
</term>
<listitem>
<para>Write output in MSF format (default FASTA)</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-log[a] <replaceable>logfile</replaceable></option>
</term>
<listitem>
<para>Log to file (append if -loga, overwrite if -log)</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-quiet</option>
</term>
<listitem>
<para>Do not write progress messages to stderr</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-stable</option>
</term>
<listitem>
<para>Output sequences in input order (default is -group)</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-group</option>
</term>
<listitem>
<para>Group sequences by similarity (this is the default)</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-version</option>
</term>
<listitem>
<para>Display version information and exit</para>
</listitem>
</varlistentry>
</variablelist>
</refsect1>
<refsect1>
<title>SEE ALSO</title>
<para>clustalw (1), seaview (1).</para>
</refsect1>
<refsect1>
<title>AUTHOR</title>
<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>
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