[Bioperl-l] PAML parsing

[Jason Stajich]

Building off of what Aaron put into place after my first attempt at
parsing in PAML reports, I've added more capabilities to the
Bio::Tools::Phylo::PAML parser beyond just pairwise Ka/Ks.

You can parse codeml and aaml output and parse NSSites models now.
It will still be undergoing some more testing to insure I've not dropped
anything, and it doesn't actually snarf up every single bit of data from
reports, but I think it is getting closer to having a solid representation
of the critical data in the various reports formats.

I'm still tinkering with the API as I give it a workout on real data
questions.  I added tests in t/PAML.t which hopefully illustrate the
new things until I can add them to the PAML HOWTO and the SYNOPSIS.

-jason
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu