Alignment Tools

[gert thijs]

I'm starting a Ph.D. on Bioinformatics and I'm wondering if there is any source
code available of a sequence alignment tool (local and global). I would like to
integrate the alignment in a search-engine. I know there are a lot of alignment
tools available on the internet, but I've to find the right one.
I've downloaded BioPerl, which seems very usefull, but it's quite huge and
rather difficult to find the right functions to do an alignment of 2 sequences. 

gert thijs

gert.thijs at esat.kuleuven.ac.be