[Biopython-dev] Parsing PAML supplementary output

Brandon Invergo b.invergo at gmail.com
Mon Oct 10 13:22:18 UTC 2011

Hi Peter

> That's because we moved to RedMine, there should have
> been a link on the old Bugzilla page, but anyway its here:
> https://redmine.open-bio.org/projects/biopython

Ok, I'll file an enhancement request there. I didn't see a link on the
Bugzilla page and there are still some links to Bugzilla on the wiki,
like in the "What's being worked on" section. I missed the Issue Tracker
link on the left (incidentally, I think this is a design problem of the
typical wiki layout and not Biopython-specific...I never notice the
contents of that list), so it might be advisable to include the link
under the Contribute heading of the main page.

> If you can extend the current PHYLIP parser (strict or relaxed)
> to cover interleaved and sequential, that would be nice. For
> strict mode at least, we can in principle follow whatever the
> original PHYLIP tools do to detect this automatically. It may
> be safer to make it explicit though - from what I recall without
> seeing the PHYLIP implementation's source code it was not
> obvious how to do this reliably.

Ok, I'll take a look at the PHYLIP source code to see how they do it

I'll report back with problems/notable progress/questions.


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