[Biojava-l] Create MSA from a profile hmm

[ckol at iti.gr]

Hello all,

I'm new in biojava and i reached a problem.
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