Hi,
I am trying to use BioJava for doing alignment between two sequences. I tried to use the pairwiseDP class, but it is not clear to me how to construct a MarkovModel for it. The problem, I think, is specifying the emission distributions for pair symbols with gaps. How can you create a pairDistribution with with a gap as an element of the distribution for use in the pairwiseDP? If anyone can refer me to example that uses pairwiseDP I would be grateful.
Another question I have is why is there no BaumWelch algorithm for MarkovModels with two heads?
Many thanks, Tal Blum _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
