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Issue #3217 has been updated by Peter Cock.
<ul>
<li><strong>Status</strong> changed from <i>In Progress</i> to <i>Closed</i></li>
<li><strong>% Done</strong> changed from <i>20</i> to <i>100</i></li>
</ul>
<p>Belatedly closing this issue - Thanks to the efforts of Ben Morris, as of Biopython 1.62 the Phylo module supports NeXML</p>
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<h1><a href="https://redmine.open-bio.org/issues/3217#change-15326">Feature #3217: Bio.Phylo I/O support for the NeXML format</a></h1>
<ul><li>Author: Eric Talevich</li>
<li>Status: Closed</li>
<li>Priority: Normal</li>
<li>Assignee: Biopython Dev Mailing List</li>
<li>Category: Main Distribution</li>
<li>Target version: Not Applicable</li>
<li>URL: </li></ul>
<p>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.</p>
Notes:
<ul>
<li>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.</li>
<li>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.</li>
</ul>
<p>See:<br /><a class="external" href="http://nexml.org/">http://nexml.org/</a><br /><a class="external" href="http://packages.python.org/DendroPy/">http://packages.python.org/DendroPy/</a><br /><a class="external" href="http://www.rdflib.net/">http://www.rdflib.net/</a></p>
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