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.