[Biopython-dev] [Biopython (old issues only) - Feature #3194] (Closed) Bio.Phylo export to 'ape' via Rpy2

[redmine at redmine.open-bio.org]

Issue #3194 has been updated by Peter Cock.

Status changed from In Progress to Closed
% Done changed from 20 to 100

Since we're aiming to turn off the RedMine server, I'm closing this and leave it to you to decide if the old patch is still useful. Thanks.

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Feature #3194: Bio.Phylo export to 'ape' via Rpy2
https://redmine.open-bio.org/issues/3194#change-15330

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

---Files--------------------------------
feat3194.diff (1.37 KB)


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