man muscle (Commandes) - Multiple Protein Sequence Alignment
NAME
muscle - Multiple Protein Sequence Alignment
SYNOPSIS
DESCRIPTION
This manual page documents briefly the muscle command.
This manual page was written for the Debian distribution because the original program does not have a manual page.
muscle aligns protein sequences and is considered superior and faster than clustalw.
OPTIONS
- -in input file
- Path to FASTA formatted input file
- -out output file
- Path to output file, FASTA formatted by default.
- -maxiters n
- Maximum number of iterations (integer, default 16)
- -maxhours n
- Maximum time to iterate in hours (default no limit)
- -clw
- Write output in CLUSTALW format (default FASTA)
- -clwstrict
- As -clw, with 'CLUSTAL W (1.81)' header
- -html
- Write output in HTML format (default FASTA)
- -msf
- Write output in MSF format (default FASTA)
- -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).
AUTHOR
This manual page was written by Steffen Moeller <moeller@pzr.uni-rostock.de> for the Debian system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation.
On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.
AUTHOR
Steffen Moeller.