- 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]
muscle aligns protein sequences and is considered superior and faster than Clustal W.
-in input file
- Path to FASTA formatted input file
-out output file
- Path to output file, FASTA formatted by default
- Find diagonals (faster for similar sequences)
- Maximum number of iterations (integer, default 16)
- Maximum time to iterate in hours (default no limit)
- Maximum memory to allocate in Mb (default 80% of RAM)
- Write output in HTML format (default FASTA)
- Write output in MSF format (default FASTA)
- Write output in Clustal W format (default FASTA)
- As -clw, with 'CLUSTAL W (1.81)' header
- Log to file (append if -loga, overwrite if -log)
- Do not write progress messages to stderr
- Output sequences in input order (default is -group)
- Group sequences by similarity (this is the default)
- Display version information and exit
- Wrote Muscle.
Steffen Moeller <[email protected]>
- Wrote this manpage.
Charles Plessy <[email protected]>
- Updated this manpage.
COPYRIGHTCopyright © 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.