[Biojava-l] Alignment with GAPs

[Dickson S. Guedes]

Hi Mark,

Ok. I´ll test it, thanks.

Curious? :) ... I´m testing somethings about progressive alignment, 
because I dont´t found how to do Multiple Sequence Aligments (MSA) using 
with only Biojava. I´m wrong?

I make some tests with strap but it´s not what I need. Have you any 
suggestion about MSA with BioJava?

Thanks all!

mark.schreiber at novartis.com escreveu:
> Hi -
> 
> I think the DP class should accept a GappedSequence. To get the result you 
> want you will probably need to have at least one match state that can emit 
> gaps. I'm curious to know why you would want to do that kind of alignment 
> though?
> 
> - Mark