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
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.
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.
Output file formats