[Biopython-dev] [Wg-phyloinformatics] GSoC Weekly Update 9: PhyloXML for Biopython

Cymon Cox cy at cymon.org
Tue Jul 21 13:01:59 UTC 2009

Hi Eric,

2009/7/21 Brad Chapman <chapmanb at 50mail.com>

> Hi Eric;


> Do you think any of the
> functionality from the Nexus trees class would fit into here and be
> useful for examining PhyloXML trees? There is a whole ton of stuff
> there but a few that caught my eye beyond the total_branch_length
> function you had a skeleton for were: get_terminals, is_identical,
> common_ancestor, and distance.
> > I haven't done anything specifically for Nexus integration, though I'm
> > looking
> > at the Bio.Nexus Tree and Node classes while writing Bio.Tree.BaseTree
> > classes.

You might also take a look at p4's tree representation and methods:

http://code.google.com/p/p4-phylogenetics/source/browse/trunk/p4/Tree.py /
Node.py / Tree_muck.py etc.

Cheers, C.

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