debian man page for muscle

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 (C) 2003, 2004 Steffen Moeller (manpage)
       Copyright (C) 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.

muscle 3.7							    02/06/2008								 MUSCLE(1)