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+.\"     Title: MUSCLE
+.\"    Author: Robert Elgar
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\"      Date: 02/06/2008
+.\"    Manual: Muscle Manual
+.\"    Source: muscle 3.7
+.\"
+.TH "MUSCLE" "1" "02/06/2008" "muscle 3.7" "Muscle Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+muscle - Multiple Protein Sequence Alignment
+.SH "SYNOPSIS"
+.HP 7
+\fBmuscle\fR \fB\-in\ \fR\fB\fIinput\ file\ (fasta)\fR\fR [\fB\-out\ \fR\fB\fIoutput\ file\ (default\ fasta)\fR\fR] [\fB\-diags\fR] [\fB\-log\ \fR\fB\fIlog\ file\fR\fR] [\fB\-maxiters\ \fR\fB\fIn\fR\fR] [\fB\-maxhours\ \fR\fB\fIn\fR\fR] [\fB\-maxmb\ \fR\fB\fIm\fR\fR] [\fB\-html\fR] [\fB\-msf\fR] [\fB\-clw\fR] [\fB\-clwstrict\fR] [\fB\-log[a]\ \fR\fB\fIlogfile\fR\fR] [\fB\-quiet\fR] [\fB\-stable\fR] [\fB\-group\fR] [\fB\-version\fR]
+.SH "DESCRIPTION"
+.PP
+This manual page documents briefly the
+\fBmuscle\fR
+command\.
+.PP
+\fBmuscle\fR
+aligns protein sequences and is considered superior and faster than Clustal\ W\.
+.SH "OPTIONS"
+.PP
+\fB\-in \fR\fB\fIinput file\fR\fR
+.RS 4
+Path to FASTA formatted input file
+.RE
+.PP
+\fB\-out \fR\fB\fIoutput file\fR\fR
+.RS 4
+Path to output file, FASTA formatted by default
+.RE
+.PP
+\fB\-diags\fR
+.RS 4
+Find diagonals (faster for similar sequences)
+.RE
+.PP
+\fB\-maxiters \fR\fB\fIn\fR\fR
+.RS 4
+Maximum number of iterations (integer, default 16)
+.RE
+.PP
+\fB\-maxhours \fR\fB\fIn\fR\fR
+.RS 4
+Maximum time to iterate in hours (default no limit)
+.RE
+.PP
+\fB\-maxmb \fR\fB\fIm\fR\fR
+.RS 4
+Maximum memory to allocate in Mb (default 80% of RAM)
+.RE
+.PP
+\fB\-html\fR
+.RS 4
+Write output in HTML format (default FASTA)
+.RE
+.PP
+\fB\-msf\fR
+.RS 4
+Write output in MSF format (default FASTA)
+.RE
+.PP
+\fB\-clw\fR
+.RS 4
+Write output in Clustal\ W format (default FASTA)
+.RE
+.PP
+\fB\-clwstrict\fR
+.RS 4
+As \-clw, with \'CLUSTAL W (1\.81)\' header
+.RE
+.PP
+\fB\-log[a] \fR\fB\fIlogfile\fR\fR
+.RS 4
+Log to file (append if \-loga, overwrite if \-log)
+.RE
+.PP
+\fB\-quiet\fR
+.RS 4
+Do not write progress messages to stderr
+.RE
+.PP
+\fB\-stable\fR
+.RS 4
+Output sequences in input order (default is \-group)
+.RE
+.PP
+\fB\-group\fR
+.RS 4
+Group sequences by similarity (this is the default)
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+Display version information and exit
+.RE
+.SH "SEE ALSO"
+.PP
+
+\fBclustalw\fR(1),
+\fBseaview\fR(1),
+\fBt_coffee\fR(1)\.
+.SH "AUTHORS"
+.PP
+\fBRobert Elgar\fR
+.sp -1n
+.IP "" 4
+Wrote Muscle\.
+.PP
+\fBSteffen Moeller\fR <\&moeller@debian\.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage\.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy\.org\&>
+.sp -1n
+.IP "" 4
+Updated this manpage\.
+.SH "COPYRIGHT"
+Copyright \(co 2003, 2004 Steffen Moeller (manpage)
+.br
+Copyright \(co 2007, 2008 Charles Plessy (manpage)
+.br
+.PP
+Muscle is in the public domain, and therefore not subjected to copyright\.
+.PP
+This manual page was written by Steffen Moeller moeller@debian\.org for the
+Debian(TM)
+system (but may be used by others)\. Permission is granted to copy, distribute and/or modify this document as if it were in public domain\.
+.sp