[Bioperl-l] protal2dna and Bio::SimpleAlign

[Maureen L Coleman]

Hi.
I'm trying to use the protal2dna script (downloaded from Pasteur site) 
to convert protein alignments back to DNA alignments. It works in some 
cases but not in others.  In the cases where it doesn't work, it pulls 
out the same sequence twice instead of pulling out seq1 and seq2 from 
my protein alignment.  Then when it tries to match it up with the 
corresponding DNA sequence, it doesn't work - it matches prot1 with 
dna1 (correctly) and prot1 with dna2 (incorrectly).

I suspect this might be related to the name,start,end (nse) method in 
Bio::SimpleAlign.  Any suggestions?

Thanks,
Maureen