|Adding sequences to an existing MSA|
To add a sequence to an existing alignment that you wish to keep intact, use profile-profile alignment with the new sequence as a profile.
muscle -profile -in1 existing_msa.afa -in2 new_seq.fa -out combined.afa
If you have more than one, you can align them first then add them, for example:
muscle -in new_seqs.fa -out new_seqs.afa
muscle -profile -in1
existing_aln.afa -in2 new_seqs.afa -out combined.afas