[Biojava-l] Using pairwiseDP

[Tal Blum]

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