Profile-profile alignment takes two existing MSAs ("profiles") and aligns them
to each other, keeping the columns in each MSA intact. The final alignment is
made by inserting columns of gaps into the MSAs as needed. The alignments of
sequences in each input MSAs are thus fully preserved in the output alignment.
One or both of the input alignments
may be single sequences.
muscle -profile -in1 one.afa -in2 two.afa
Profile-profile alignment is not
for homolog recognition
MUSCLE does not compute a similarity measure or measure of
statistical significance (such as an E-value), so this option is not useful for
discriminating homologs from unrelated sequences.