MUSCLE manual
Alignment output options
Muscle supports several alignment formats, summarized in the following table. The output format can be specified in two different ways, you can choose either (but not both). For example, the -clw option specifies that the primary output should be written in CLUSTALW format, and the -clwout option gives the name of an output file that will be written in CLUSTALW format. The primary output is specified using the -out option, and defaults to standard output.

Multiple output formats in one run
You can specify several -xxxout option on the same command line, which allows you to create multiple output formats in a single run, e.g.:

  muscle -in seqs.fa -fastaout seqs.afa -clwout seqs.aln

Flag Filename option Description
-clw -clwout filename CLUSTALW format. By default, will write MUSCLE as the program name in the file header. If the -clwstrict option is specified, then the program name will be written as "CLUSTAL W (1.81)". This is useful if the output will be parsed by scripts that check the program name.
-fasta -fastaout filename FASTA format (default).
‑html -htmlout filename HTML (web page) output. The alignment is colored using a color scheme from Eric Sonnhammer's Belvu editor.
‑phys -physout filename PHYLIP sequential format.
‑phyi -phyiout filename PHYLIP interleaved format.
‑msf -msfout filename MSF format, as used in the GCG package, is requested by using the –msf option. As with CLUSTALW format, this is easier for people to read than FASTA. As of MUSCLE 3.52, the MSF format has been tweaked to be more compatible with GCG. The following differences remain.

(a) MUSCLE truncates labels at the first white space or after 63 characters, which ever comes first. The GCG package apparently truncates after 10 characters. If this is a problem for you, please let me know and I'll add an option to truncate after 10 in a future version.

(b) MUSCLE allows duplicate sequence labels, while GCG forbids duplicates. If you use the –stable option of muscle, then the order of the input sequences is preserved and sequences can be unambiguously identified even if the labels differ.

Thanks to Eric Martel for help with improving GCG compatibility.