[Biopython-dev] [Biopython - Feature #3194] Bio.Phylo export to 'ape' via Rpy2

[redmine at redmine.open-bio.org]

Issue #3194 has been updated by Eric Talevich.

File feat3194.diff added
Estimated time changed from 0.50 to 1.00

Patch based on the cookbook entry.
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Feature #3194: Bio.Phylo export to 'ape' via Rpy2
https://redmine.open-bio.org/issues/3194

Author: Eric Talevich
Status: In Progress
Priority: Low
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: Not Applicable
URL: 


There are many more packages for working with phylogenetic data in R, and most of these operate on the basic tree object defined in the ape package. Let's support interoperability through Rpy2.

The trivial way to do this is serialize a tree to a Newick string, then feed that to the read.tree() function. Maybe we can build the tree object in R directly and retain the tree annotations that Newick doesn't handle.

See:
http://ape.mpl.ird.fr/
http://rpy.sourceforge.net/rpy2.html


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