muscle (1)

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 muscle command.

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

-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

clustalw(1), seaview(1), t_coffee(1).

Robert Elgar

• Wrote Muscle.

Steffen Moeller <[email protected]>

• Wrote this manpage.

Charles Plessy <[email protected]>

• 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 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.