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