Dear colleagues, Thank you very much for your many replies! There are a number of top hits and a few programs only mentioned once or twice. Most are free to download as well. Top hits are old favourites: MEGA (Windows) http://www.megasoftware.net BioEdit (Windows) http://www.mbio.ncsu.edu/BioEdit/bioedit.html Se-Al (Mac) http://tree.bio.ed.ac.uk/software/seal/ Others: TranslatorX (online) http://translatorx.co.uk MacClade (Mac, not free) http://macclade.org/macclade.html Mesquite (all platforms) http://mesquiteproject.org/mesquite/mesquite.html Seaview (all platforms) http://pbil.univ-lyon1.fr/software/seaview.html DAMBE (all platforms) http://dambe.bio.uottawa.ca/dambe.asp TransAlign.pl http://www.molekularesystematik.uni-oldenburg.de/33997.html Geneious (not free) http://www.geneious.com DNAsp (all platforms) http://www2.ub.es/dnasp/download.html t-coffee (all platforms or online) http://www.ebi.ac.uk/Tools/t-coffee/index.html Proseq (Windos, Linux) http://dps.plants.ox.ac.uk/sequencing/proseq.htm Mbetoolbox (all platforms) http://www.bioinformatics.org/mbetoolbox/ FAST (soon to be released by David Ardell) NB: I used BioEdit as I have already used it for manual alignment editing (I just didn't see the toggle function to protein!). Just a word of warning: the toggle function Ctl+A to select all sequences and Ctl+G or Ctr+T to toggle to protein view (and back) will not save the protein view! You need to use the dropdown menu and select the permanent translation option. And when you do this, it will 'correct' your protein for those nasty frameshifts and premature STOP codons and not tell you about it! It just inserts an 'X' for the missing residue! So you need to check your alignment carefully to find those with problems. Thanks again everyone! Happy translating, Birgit NOTE NEW PHONE NO! Birgit Meldal, Ph.D. Division of Transfusion Medicine Department of Haematology University of Cambridge NHS Blood & Transplant, Cambridge Centre Long Road Cambridge CB2 0PT U.K. +44 1223 588049 bhmm2@cam.ac.uk