[Biojava-l] Pairwise Alignment

Joanna Sharman J.L.Sharman at sms.ed.ac.uk
Wed Apr 19 09:35:14 UTC 2006


I'm new to BioJava so I'm sorry if this question has been asked several
times before.

This is actually sort of in reply to this message from last month:


I'd like to perform a simple pairwise alignment using the
Smith-Waterman class I saw described here:


but I can't find the classes it mentions anywhere on the cvs.  Can you
point me to where they are?

Also, I'm just wondering why the HMM method is preferred to the
Smith-Waterman (or others)?  It seems quite complicated to me, and like
it might require more memory, or am I wrong? :)


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