Multiple alignment program of protein sequences

Some information about Muscle from the Debian Med project.

MUSCLE is a multiple alignment program for protein sequences. MUSCLE
stands for multiple sequence comparison by log-expectation.  In the
authors tests, MUSCLE achieved the highest scores of all tested
programs on several alignment accuracy benchmarks, and is also one of
the fastest programs out there.

Homepage: http://www.drive5.com/muscle

Basic usage

    muscle -in <inputfile> -out <outputfile>

Common options (for a complete list please see the User Guide):

    -in <inputfile>    Input file in FASTA format (default stdin)
    -out <outputfile>  Output alignment in FASTA format (default stdout)
    -diags             Find diagonals (faster for similar sequences)
    -maxiters <n>      Maximum number of iterations (integer, default 16)
    -maxhours <h>      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 GCG MSF format (default FASTA)
    -clw               Write output in CLUSTALW 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

Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2
Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3
Fastest possible (nucleotides): -maxiters 1 -diags

See also:  man muscle
