[Biopython-dev] Code review request for phyloxml branch

[Eric Talevich]

On Sat, Jan 9, 2010 at 9:50 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> I think that this code can now be included with Biopython, assuming that there will be some documentation on its usage to accompany it.

OK -- I pulled the latest from biopython/biopython on GitHub, merged
my phyloxml branch into my master branch, and pushed it all back to
biopython. Bio.Phylo is now part of Biopython!

For documentation on the Biopython wiki, I moved the relevant parts of
the Tree, TreeIO and PhyloXML pages to a new page for Bio.Phylo:
http://biopython.org/wiki/Phylo

It's a little rough at the moment, but I'll refine it this week. Some
of the content can also be moved to separate cookbook entries.

> One more small thing: I noticed when looking at the source code that some comments still refer to Bio.Tree rather than Bio.Phylo -- could you fix this?

I went over all the docstrings and comments again before merging; it
should be free of Tree/TreeIO references now.

Thanks for your help!
Eric