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Issue #3134 has been updated by Peter Cock.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15392?detail_id=1727">diff</a>)</li>
<li><strong>Status</strong> changed from <i>New</i> to <i>Resolved</i></li>
<li><strong>% Done</strong> changed from <i>0</i> to <i>100</i></li>
</ul>
<p>I looks like this was resolved but the issue left open. Closing now as resolved.</p>
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<h1><a href="https://redmine.open-bio.org/issues/3134#change-15392">Bug #3134: to_networkx returns weird stuff</a></h1>
<ul><li>Author: John empty</li>
<li>Status: Resolved</li>
<li>Priority: Normal</li>
<li>Assignee: Biopython Dev Mailing List</li>
<li>Category: Main Distribution</li>
<li>Target version: 1.55b</li>
<li>URL: </li></ul>
<p>Hi,</p>
<p>I tried to read <br /><a class="external" href="http://www.phylosoft.org/archaeopteryx/examples/data/multiple_supports.xml">http://www.phylosoft.org/archaeopteryx/examples/data/multiple_supports.xml</a> <br />and convert it using to_networkx(). Strangely, all nodes in the resulting graph are named Clade, and when using networkx.write_dot() I get a file with a single clade node, although the number of nodes in the graph object is correct. Also using networkx.to_agraph() does not help.</p>
<p>tree = Phylo.read("multiple_support.xml", "phyloxml")<br />tree = Phylo.to_networkx(tree)<br />print set(tree.nodes())<br />print tree.number_of_nodes()<br />networkx.write_dot(tree, "test.dot")<br />tree = networkx.to_agraph(tree)<br />tree.draw("tree.pdf", prog = "dot")</p>
<p>For <a class="external" href="http://www.phylosoft.org/archaeopteryx/examples/data/bcl_2.xml">http://www.phylosoft.org/archaeopteryx/examples/data/bcl_2.xml</a> I get a star tree with a single Clade node in the center and leafs labeled by gene names.</p>
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