&dhtitle;

&dhpackage;
&dhrelease;
Robert C. Elgar Wrote Muscle.
&dhfirstname; &dhsurname; Wrote this manpage.

    &dhemail;

Charles Plessy Updated this manpage.

    charles-debian-nospam@plessy.org

2003 2004 &dhusername; (manpage)
2007 2008 Charles Plessy (manpage)

Muscle is in the public domain, and therefore not subjected to copyright.

This manual page was written by &dhusername; &dhemail; for the &debian; 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.

&dhucpackage; &dhsection;
&dhpackage; Multiple Protein Sequence Alignment
`&dhpackage;` `-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 `&dhpackage;` command.

`&dhpackage;` 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 .