[Biopython-dev] Parsing PAML supplementary output

[Brandon Invergo]

Hi all,
I've received a request to implement the parsing of the main
supplementary output files of the PAML programs ('rst' files). I can't
submit a bug on Bugzilla, so I'll just announce my intention to work on
this here on the list.

One question though. The rst file for baseml includes an alignment which
is in the Phylip sequential format. I thought that it would be nice to
parse that directly into a Biopython MultipleSeqAlignment. It's my
understanding that Biopython only supports the interleaved format. Would
it be worth it for me to extend that functionality to include the
sequential format or would it be preferable to convert the alignments to
be interleaved within the parser itself?

Regards,
Brandon Invergo