A number of people wanted to see the responses I got in looking for software that can translate an alignment into amino acids, align based on on amino acids, and back translate to the original DNA sequences. Two PC - only programs seems the most commonly used, MEGA and BioEdit but a number of other programs were also suggested. here they are.... MEGA - PC and linux BioEdit -PC RevTrans http://www.cbs.dtu.dk/services/RevTrans/ Genious - there is a freeware version, but I don't know yet whether the freeware version includes this function. DAMBE -PC and LInux PAL2NAL http://coot.embl.de/pal2nal/ Bioperl toolkit TransAlign http://www.biomedcentral.com/1471-2105/6/156 aa2dna http://www.bio.psu.edu/People/Faculty/Nei/Lab/software.htm Biopython MacClade DNAstar (not free) Prank/ Prankster: http://www.ebi.ac.uk/goldman-srv/prank SeaView http://pbil.univ-lyon1.fr/software/seaview.html Christopher Balakrishnan Institute for Genomic Biology University of Illinois phone: 617-905-2910 https://netfiles.uiuc.edu/cbala/www/ Christopher Balakrishnan