[Bioperl-l] Getting pairwise alignment scores for existing multiple alignment

[Alexey Morozov]

Dear colleagues,
Is there a method in bioperl that will calculate pairwise alignment scores
for any given pair of genes in MSA (according to a given matrix and gap
opening/extension cost)? It seems that Bio::SimpleAlign methods only work
with score if it has been described in MSA file and can only hold a general
multiple sequence alignment score.

-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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