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.