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

[redmine at redmine.open-bio.org]

Issue #3194 has been updated by Eric Talevich.

Status changed from New to In Progress
Assignee changed from Eric Talevich to Biopython Dev Mailing List
% Done changed from 0 to 20
Estimated time set to 0.50

I added a cookbook entry for this on the Biopython wiki:

http://www.biopython.org/wiki/Phylo_cookbook#Convert_to_an_.27ape.27_tree.2C_via_Rpy2

Good enough? Trying it in ipython, it works as advertised, except after calling r.plot() the R plot window won't close until I exit ipython. Further calls to plot() update the window; it just doesn't close.
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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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