Have a look a GeneDoc. It wont create an alignment program for you, clustalw can do that, but you can then edit, shade and annotate the alignment. http://www.cris.com/~Ketchup/genedoc.shtml >Hello, >I was wondering if anybody knows a nice sequence alignmment >program that runs on a PC? >Thanks for your help! >Cheers, > Agustin