[Bioperl-l] Multiple alignments and Biographics

[Sean Davis]

Dear all,

I am interested in forming multiple alignments between transcripts from the
same gene cluster and rendering them using biographics.  I have alignments
(from blast) from a set of oligos that I then want to include in the
alignment.  Since multiple alignments do not have a "reference" sequence in
this case, can anyone give me ideas about how to approach the problem with
biographics?  

Thanks,
Sean