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.