muscle(1) 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 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


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)


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[a] logfile

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


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.