Man page - muscle3(1)

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Manual

MUSCLE

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
AUTHORS
COPYRIGHT

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

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

AUTHORS

Robert Elgar

Wrote Muscle.

Steffen Moeller <moeller@debian.org>

Wrote this manpage.

Charles Plessy <charles-debian-nospam@plessy.org>

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 moeller@debian.org 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.