Hi,

I have an alignment between 4 proteins and I want to add each protein's sequence homolgs to it. Is there a tool where I can label my original alignment as a "core alignment" and not change it, and have the homolgs align according to this alignment?

Thanks!
MAFFT lets you do this with the `--add_sequence` option: http://mafft.cbrc.jp/alignment/software/addsequences.html

Quite good alignment software, and I've used this option many times to add new sequences to existing alignments.