[Biojava-l] Pairwise Alignment

[Joanna Sharman]

Hello,

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:

http://lists.open-bio.org/pipermail/biojava-l/2006-March/005365.html

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

http://www.biojava.org/wiki/BioJava:CookBook:DP:PairWise2

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? :)

Cheers,
Joanna