MUSCLE manual
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.

You have an existing alignment existing_msa.afa and want to add a new sequence in new_seq.fa.

   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