Provided by: muscle_3.8.31-1_amd64 bug


       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 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


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


       Robert Elgar
           Wrote Muscle.

       Steffen Moeller <>
           Wrote this manpage.

       Charles Plessy <>
           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 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.