[Biojava-l] Multiple Sequence Alignment with Profile HMMs

[Chrysa Collyda]

Hello all,

I would like to pose again a question regarding multiple sequence alignment with profile HMMs. Any help would be deeply appreciated. 

i created a profile hmm from a set of unaligned homologues sequences then
i aligned some sequences to the model.i noticed that every sequence has
its own length for the alignment.is there any method by which i can create
a multiple sequence alignment between these sequences?


        thanks in advance,
        ckol