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
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.