[Biojava-dev] Reading a Profile from a FASTA file

[Spencer Bliven]

I have a FASTA file containing a multiple sequence alignment (using '-' for
gaps). What is the easiest way to work with this in biojava?

   1. It seems like a Profile<S,C> is the correct interface for working with
   multiple sequence alignments. However, the only implementation I found is
   SimpleProfile, which doesn't have any methods for adding more than two
   sequences to the profile. Do I need to create my own implementation of
   Profile to allow arbitrarily many AlignedSequences to be stored?
   2. FastaReader is useful for getting a Set of Sequences from a FASTA
   file. Is there any existing way to convert this into a Profile or other
   standard object?

Apologies if I'm missing something obvious here...

Thanks!
-Spencer