[Biojava-l] HMM Alignments.

[Thomas Down]

Hi...

Has anyone yet looked at Matthew Pocock's Hidden Markov
Model code, currently found in the org.biojava.bio.alignment
package?

Currently, it offers a fairly flexible framework for HMMs
which model a single sequence.  However, I'm looking at some
problems where I would like to be able to evaluate pair-HMMs.
This means some API changes/additions are needed in order
to support HMM states which can emit residues for more than
one sequence (although pair HMMs are my priority, it seems
kind-of nice to allow arbitratry numbers of sequences).

I'll see if I can come up with some revised interfaces in the
next couple of days, but if anyone else has any strong feelings
about how this should be done, suggestions are welcomed.

Thanks,

Thomas.
-- 
``He returned with milk, flour, sugar... and incidentally,
a new body.''   -- Octavia Butler