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
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
AUTHORS
Robert Elgar
- Wrote Muscle.
Steffen Moeller <[email protected]>
- Wrote this manpage.
Charles Plessy <[email protected]>
- 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 [email protected] 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.