Make an alignment and save to a file in FASTA format:

  muscle -in seqs.fa -out seqs.afa

Write alignment to the console in CLUSTALW format (more readable than FASTA):

  muscle -in seqs.fa -clw

Input file
Specified using the -in option. Must be in FASTA format. If any gaps are present in the input file, they will be discarded before making the alignment. If the -in option is not specified, or is specified as - (a minus sign), then input is taken from standard input.

Output file
Specified using the -out option. By default, the output is in FASTA format with gaps added to align the sequences. If the -out option is not specified, or is specified as - (minus sign), then output is written to standard output. I use "afa" (aligned fasta) as the conventional filename extension.

See also
  Output file formats
  Iterations