As well as all the other suggestions, SeaView allows you to select any sites (columns) in the alignment and save them to a new file. Useful if you want to extract multiple non-adjacent regions from an alignment. http://pbil.univ-lyon1.fr/software/seaview.html -- Dr. Roy Chaudhuri Bioinformatics Research Fellow, Division of Immunity and Infection, University of Birmingham, UK http://colibase.bham.ac.uk