Hi All, I have a database of about 400 squences, which I want to compare All-vs-All to get the global alignment score of each protein sequence pair. I tried using bl2seq but that gives me local alignments. What other program would suit this function best ? I would probably like to have the flexibility of being able to use various matrices. Thanks a lot, -Manisha -------------- next part -------------- An HTML attachment was scrubbed... URL: http://bioinformatics.org/pipermail/ssml-general/attachments/20050110/a8dd65b5/attachment.htm