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MUSCLE(1) Muscle Manual MUSCLE(1)

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.
 
02/06/2008 muscle 3.7