[Biopython-dev] [Biopython (old issues only) - Feature #3217] (Closed) Bio.Phylo I/O support for the NeXML format

[redmine at redmine.open-bio.org]

Issue #3217 has been updated by Peter Cock.

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

Belatedly closing this issue - Thanks to the efforts of Ben Morris, as of Biopython 1.62 the Phylo module supports NeXML

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Feature #3217: Bio.Phylo I/O support for the NeXML format
https://redmine.open-bio.org/issues/3217#change-15326

* Author: Eric Talevich
* Status: Closed
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: Not Applicable
* URL: 
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The future data exchange standard is... approaching rapidly. NeXML is going to become the format of choice for TreeBASE, Mesquite and probably MIAPA-targeted tools over the next year or two, and Biopython should be there to support it.

Notes:
* Another Python library, DendroPy, already supports (some of?) the NeXML format. Jeet Sukumaran and Mark Holder changed the license to BSD to allow other projects -- particularly us -- to share their code. So let's start there.
* NeXML was designed so its elements can be treated as RDF triples, so see if RDFLib can help -- either as the underlying parser, or to provide some additional (optional) functionality.

See:
http://nexml.org/
http://packages.python.org/DendroPy/
http://www.rdflib.net/



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