Hi, Do we have a pairwise alignment module which can use scoring matrices? I only know of Bio.pairwise2 which uses a match/mismatch scoring scheme. Thanks, Iddo -- Iddo Friedberg The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171