MUSCLE v3.8.31 by Robert C. Edgar

This software is donated to the public domain.
Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.

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)
    -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
    -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

More information at the [[ Muscle home page]]