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MUSCLE

MUSCLE

Section: Muscle Manual (1) Updated: 02/06/2008
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NAME

muscle - Multiple Protein Sequence Alignment  

SYNOPSIS

muscle -in input file (fasta) [-out output file (default fasta)] [-diags] [-log log file] [-maxiters n] [-maxhours n] [-maxmb m] [-html] [-msf] [-clw] [-clwstrict] [-log[a] logfile] [-quiet] [-stable] [-group] [-version]
 

DESCRIPTION

This manual page documents briefly the muscle command.

muscle aligns protein sequences and is considered superior and faster than Clustal W.  

OPTIONS

-in input file

Path to FASTA formatted input file

-out output file

Path to output file, FASTA formatted by default

-diags

Find diagonals (faster for similar sequences)

-maxiters n

Maximum number of iterations (integer, default 16)

-maxhours n

Maximum time to iterate in hours (default no limit)

-maxmb m

Maximum memory to allocate in Mb (default 80% of RAM)

-html

Write output in HTML format (default FASTA)

-msf

Write output in MSF format (default FASTA)

-clw

Write output in Clustal W format (default FASTA)

-clwstrict

As -clw, with 'CLUSTAL W (1.81)' header

-log[a] logfile

Log to file (append if -loga, overwrite if -log)

-quiet

Do not write progress messages to stderr

-stable

Output sequences in input order (default is -group)

-group

Group sequences by similarity (this is the default)

-version

Display version information and exit
 

SEE ALSO

clustalw(1), seaview(1), t_coffee(1).  

AUTHORS

Robert Elgar

Wrote Muscle.

Steffen Moeller <moeller@debian.org>

Wrote this manpage.

Charles Plessy <charles-debian-nospam@plessy.org>

Updated this manpage.
 

COPYRIGHT

Copyright © 2003, 2004 Steffen Moeller (manpage)
Copyright © 2007, 2008 Charles Plessy (manpage)

Muscle is in the public domain, and therefore not subjected to copyright.

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.


 

Index

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
AUTHORS
COPYRIGHT

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Time: 21:24:08 GMT, April 16, 2011