muscle - Multiple Protein Sequence Alignment

RobertElgar
           Wrote Muscle.

       SteffenMoeller <moeller@debian.org>

           Wrote this manpage.

       CharlesPlessy <charles-debian-nospam@plessy.org>
           Updated this manpage.

       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.

muscle 3.7                                         02/06/2008                                          MUSCLE(1)

       This manual page documents briefly the muscle command.

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

       muscle - Multiple Protein Sequence Alignment

-ininputfile
           Path to FASTA formatted input file

       -outoutputfile
           Path to output file, FASTA formatted by default

       -diags
           Find diagonals (faster for similar sequences)

       -maxitersn
           Maximum number of iterations (integer, default 16)

       -maxhoursn
           Maximum time to iterate in hours (default no limit)

       -maxmbm
           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

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

muscle-ininputfile(fasta) [-outoutputfile(defaultfasta)] [-diags] [-loglogfile] [-maxitersn]
              [-maxhoursn] [-maxmbm] [-html] [-msf] [-clw] [-clwstrict] [-log[a]logfile] [-quiet] [-stable]
              [-group] [-version]