I'm interested in aligning a population of related protein sequences against a canonical reference. This doesn't seem to fit into either of the major categories of alignment packages: it's neither pairwise alignment nor multiple sequence alignment. The main problem is that I don't want to allow the aligner to "delete" residues in the reference: every aligned sequence should be the same length as the reference. Perhaps this can be done within existing MSA programs (like clustal and MAFFT) but it's not obvious to me how to do it. Can someone help out?