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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
