Bioperl works I think. I know that internall Pfam runs off a branched copy
of bioperl, but it was branched about 2 years ago (when I left the Pfam
group...) so no promises.
Bio::AlignIO is what you are looking for...
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<[EMAIL PROTECTED]>.
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