> OK - so you have a single HMM that emits whole columns of an alignment?
> Usually to a lign three sequences, you would use a 3-head HMM where each head
> emits one of the sequences.
I am not sure if it would work with a 3 head HMM, as in here the
sequences are related to each other by the phylogenetic tree. so if
the sequences order is the same, the column ACC would have a different
likelihood than CCA.
> You shouldn't be getting exceptions. This is almost certainly a bug. Could you
> send the stack-trace?
sure, here it is:
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0
I think I don't need the full alphabet of getDNA(), which has 16
symbols. I reduced it to 5 (A,T, C, G, N), so I can have a state that
contains more sites...