[Biojava-l] Multiple sequence alignment

[hlr02 at doc.ic.ac.uk]

Hi,

I am aligning a set of sequences to a profile HMM. I would like to convert the 
individual alignments into one (multiple sequence) alignment object. I tried to 
build a new map for my msa by retrieving the sequence symbollist from the 
statepaths and the sequence names. The problem with this approach is that the 
symbollists differ in length and the alignments haven't been 'zipped' to take 
redundant gaps into account.

I was wondering if biojava supports conversion of a set of alignments into a 
multiple sequence alignment so that all alignments will have the same length.

Thanks,

Henry Romijn