Section: Muscle Manual (1) Updated: 02/06/2008 Local index
muscle - Multiple Protein Sequence Alignment
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]
This manual page documents briefly the
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
Steffen Moeller < email@example.com>
Wrote this manpage.
Charles Plessy < firstname.lastname@example.org>
Updated this manpage.
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@example.com for the
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.
This document was created by
using the manual pages.
Time: 21:24:08 GMT, April 16, 2011