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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Nexus-module.html">Package Nexus</a> ::
<a href="Bio.Nexus.Trees-module.html">Module Trees</a> ::
Class Tree
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Tree</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree">source code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="Bio.Nexus.Nodes.Chain-class.html">Nodes.Chain</a> --+
|
<strong class="uidshort">Tree</strong>
</pre>
<hr />
<p>Represents a tree using a chain of nodes with on predecessor
(=ancestor) and multiple successors (=subclades).</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td align="left"><span class="table-header">Instance Methods</span></td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">tree</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">weight</span>=<span class="summary-sig-default">1.0</span>,
<span class="summary-sig-arg">rooted</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">name</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">data</span>=<span class="summary-sig-default"><class 'Bio.Nexus.Trees.NodeData'></span>,
<span class="summary-sig-arg">values_are_support</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">max_support</span>=<span class="summary-sig-default">1.0</span>)</span><br />
Ntree(self,tree).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.__init__">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_parse"></a><span class="summary-sig-name">_parse</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">tree</span>)</span><br />
Parses (a,b,c...)[[[xx]:]yy] into subcomponents and travels down
recursively.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree._parse">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#_add_subtree" class="summary-sig-name" onclick="show_private();">_add_subtree</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">parent_id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">tree</span>=<span class="summary-sig-default">None</span>)</span><br />
Adds leaf or tree (in newick format) to a parent_id.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree._add_subtree">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_add_nodedata"></a><span class="summary-sig-name">_add_nodedata</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">nd</span>,
<span class="summary-sig-arg">st</span>)</span><br />
Add data to the node parsed from the comments, taxon and support.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree._add_nodedata">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="_get_values"></a><span class="summary-sig-name">_get_values</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">text</span>)</span><br />
Extracts values (support/branchlength) from xx[:yyy], xx.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree._get_values">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_walk"></a><span class="summary-sig-name">_walk</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">node</span>=<span class="summary-sig-default">None</span>)</span><br />
Return all node_ids downwards from a node.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree._walk">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#node" class="summary-sig-name">node</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">node_id</span>)</span><br />
Return the instance of node_id.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.node">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#split" class="summary-sig-name">split</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">parent_id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">n</span>=<span class="summary-sig-default">2</span>,
<span class="summary-sig-arg">branchlength</span>=<span class="summary-sig-default">1.0</span>)</span><br />
Speciation: generates n (default two) descendants of a node.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.split">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#search_taxon" class="summary-sig-name">search_taxon</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">taxon</span>)</span><br />
Returns the first matching taxon in self.data.taxon.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.search_taxon">source code</a></span>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#prune" class="summary-sig-name">prune</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">taxon</span>)</span><br />
Prunes a terminal taxon from the tree.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.prune">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#get_taxa" class="summary-sig-name">get_taxa</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">node_id</span>=<span class="summary-sig-default">None</span>)</span><br />
Return a list of all otus downwards from a node (self, node_id).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.get_taxa">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="get_terminals"></a><span class="summary-sig-name">get_terminals</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return a list of all terminal nodes.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.get_terminals">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="is_terminal"></a><span class="summary-sig-name">is_terminal</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">node</span>)</span><br />
Returns True if node is a terminal node.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_terminal">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="is_internal"></a><span class="summary-sig-name">is_internal</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">node</span>)</span><br />
Returns True if node is an internal node.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_internal">source code</a></span>
</td>
</tr>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="is_preterminal"></a><span class="summary-sig-name">is_preterminal</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">node</span>)</span><br />
Returns True if all successors of a node are terminal ones.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_preterminal">source code</a></span>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="count_terminals"></a><span class="summary-sig-name">count_terminals</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">node</span>=<span class="summary-sig-default">None</span>)</span><br />
Counts the number of terminal nodes that are attached to a node.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.count_terminals">source code</a></span>
</td>
</tr>
</table>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<td><span class="summary-sig"><a name="collapse_genera"></a><span class="summary-sig-name">collapse_genera</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">space_equals_underscore</span>=<span class="summary-sig-default">True</span>)</span><br />
Collapses all subtrees which belong to the same genus (i.e share the
same first word in their taxon name.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.collapse_genera">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#sum_branchlength" class="summary-sig-name">sum_branchlength</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">root</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">node</span>=<span class="summary-sig-default">None</span>)</span><br />
Adds up the branchlengths from root (default self.root) to node.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.sum_branchlength">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#set_subtree" class="summary-sig-name">set_subtree</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">node</span>)</span><br />
Return subtree as a set of nested sets.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.set_subtree">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#is_identical" class="summary-sig-name">is_identical</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">tree2</span>)</span><br />
Compare tree and tree2 for identity.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_identical">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#is_compatible" class="summary-sig-name">is_compatible</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">tree2</span>,
<span class="summary-sig-arg">threshold</span>,
<span class="summary-sig-arg">strict</span>=<span class="summary-sig-default">True</span>)</span><br />
Compares branches with support>threshold for compatibility.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_compatible">source code</a></span>
</td>
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</td>
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<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#common_ancestor" class="summary-sig-name">common_ancestor</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">node1</span>,
<span class="summary-sig-arg">node2</span>)</span><br />
Return the common ancestor that connects two nodes.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.common_ancestor">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#distance" class="summary-sig-name">distance</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">node1</span>,
<span class="summary-sig-arg">node2</span>)</span><br />
Add and return the sum of the branchlengths between two nodes.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.distance">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#is_monophyletic" class="summary-sig-name">is_monophyletic</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">taxon_list</span>)</span><br />
Return node_id of common ancestor if taxon_list is monophyletic, -1
otherwise.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_monophyletic">source code</a></span>
</td>
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</table>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="is_bifurcating"></a><span class="summary-sig-name">is_bifurcating</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">node</span>=<span class="summary-sig-default">None</span>)</span><br />
Return True if tree downstream of node is strictly bifurcating.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_bifurcating">source code</a></span>
</td>
</tr>
</table>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#branchlength2support" class="summary-sig-name">branchlength2support</a>(<span class="summary-sig-arg">self</span>)</span><br />
Move values stored in data.branchlength to data.support, and set
branchlength to 0.0</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.branchlength2support">source code</a></span>
</td>
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</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#convert_absolute_support" class="summary-sig-name">convert_absolute_support</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">nrep</span>)</span><br />
Convert absolute support (clade-count) to rel.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.convert_absolute_support">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="has_support"></a><span class="summary-sig-name">has_support</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">node</span>=<span class="summary-sig-default">None</span>)</span><br />
Returns True if any of the nodes has data.support != None.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.has_support">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#randomize" class="summary-sig-name">randomize</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">ntax</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">taxon_list</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">branchlength</span>=<span class="summary-sig-default">1.0</span>,
<span class="summary-sig-arg">branchlength_sd</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">bifurcate</span>=<span class="summary-sig-default">True</span>)</span><br />
Generates a random tree with ntax taxa and/or taxa from taxlabels.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.randomize">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="display"></a><span class="summary-sig-name">display</span>(<span class="summary-sig-arg">self</span>)</span><br />
Quick and dirty lists of all nodes.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.display">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#to_string" class="summary-sig-name">to_string</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">support_as_branchlengths</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">branchlengths_only</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">plain</span>=<span class="summary-sig-default">True</span>,
<span class="summary-sig-arg">plain_newick</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">ladderize</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">ignore_comments</span>=<span class="summary-sig-default">True</span>)</span><br />
Return a paup compatible tree line.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.to_string">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Short version of to_string(), gives plain tree</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.__str__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="unroot"></a><span class="summary-sig-name">unroot</span>(<span class="summary-sig-arg">self</span>)</span><br />
Defines a unrooted Tree structure, using data of a rooted Tree.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.unroot">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="root_with_outgroup"></a><span class="summary-sig-name">root_with_outgroup</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">outgroup</span>=<span class="summary-sig-default">None</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.root_with_outgroup">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#merge_with_support" class="summary-sig-name">merge_with_support</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">bstrees</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">constree</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">threshold</span>=<span class="summary-sig-default">0.5</span>,
<span class="summary-sig-arg">outgroup</span>=<span class="summary-sig-default">None</span>)</span><br />
Merges clade support (from consensus or list of bootstrap-trees) with
phylogeny.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.merge_with_support">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Nexus.Nodes.Chain-class.html">Nodes.Chain</a></code></b>:
<code><a href="Bio.Nexus.Nodes.Chain-class.html#add">add</a></code>,
<code><a href="Bio.Nexus.Nodes.Chain-class.html#all_ids">all_ids</a></code>,
<code><a href="Bio.Nexus.Nodes.Chain-class.html#collapse">collapse</a></code>,
<code><a href="Bio.Nexus.Nodes.Chain-class.html#is_parent_of">is_parent_of</a></code>,
<code><a href="Bio.Nexus.Nodes.Chain-class.html#kill">kill</a></code>,
<code><a href="Bio.Nexus.Nodes.Chain-class.html#link">link</a></code>,
<code><a href="Bio.Nexus.Nodes.Chain-class.html#trace">trace</a></code>,
<code><a href="Bio.Nexus.Nodes.Chain-class.html#unlink">unlink</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Nexus.Nodes.Chain-class.html">Nodes.Chain</a></code></b> (private):
<code><a href="Bio.Nexus.Nodes.Chain-class.html#_get_id" onclick="show_private();">_get_id</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">tree</span>=<span class="sig-default">None</span>,
<span class="sig-arg">weight</span>=<span class="sig-default">1.0</span>,
<span class="sig-arg">rooted</span>=<span class="sig-default">False</span>,
<span class="sig-arg">name</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>,
<span class="sig-arg">data</span>=<span class="sig-default"><class 'Bio.Nexus.Trees.NodeData'></span>,
<span class="sig-arg">values_are_support</span>=<span class="sig-default">False</span>,
<span class="sig-arg">max_support</span>=<span class="sig-default">1.0</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.__init__">source code</a></span>
</td>
</tr></table>
<p>Ntree(self,tree).</p>
<dl class="fields">
<dt>Overrides:
object.__init__
</dt>
</dl>
</td></tr></table>
</div>
<a name="_add_subtree"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_add_subtree</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">parent_id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">tree</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree._add_subtree">source code</a></span>
</td>
</tr></table>
<p>Adds leaf or tree (in newick format) to a parent_id.
(self,parent_id,tree).</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="node"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">node</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">node_id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.node">source code</a></span>
</td>
</tr></table>
<p>Return the instance of node_id.</p>
<p>node = node(self,node_id)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="split"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">split</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">parent_id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">n</span>=<span class="sig-default">2</span>,
<span class="sig-arg">branchlength</span>=<span class="sig-default">1.0</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.split">source code</a></span>
</td>
</tr></table>
<p>Speciation: generates n (default two) descendants of a node.</p>
<p>[new ids] = split(self,parent_id=None,n=2,branchlength=1.0):</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="search_taxon"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">search_taxon</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">taxon</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.search_taxon">source code</a></span>
</td>
</tr></table>
<p>Returns the first matching taxon in self.data.taxon. Not restricted to
terminal nodes.</p>
<p>node_id = search_taxon(self,taxon)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="prune"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">prune</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">taxon</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.prune">source code</a></span>
</td>
</tr></table>
<p>Prunes a terminal taxon from the tree.</p>
<p>id_of_previous_node = prune(self,taxon) If taxon is from a
bifurcation, the connectiong node will be collapsed and its branchlength
added to remaining terminal node. This might be no longer a meaningful
value'</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="get_taxa"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">get_taxa</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">node_id</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.get_taxa">source code</a></span>
</td>
</tr></table>
<p>Return a list of all otus downwards from a node (self, node_id).</p>
<p>nodes = get_taxa(self,node_id=None)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="sum_branchlength"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">sum_branchlength</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">root</span>=<span class="sig-default">None</span>,
<span class="sig-arg">node</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.sum_branchlength">source code</a></span>
</td>
</tr></table>
<p>Adds up the branchlengths from root (default self.root) to node.</p>
<p>sum = sum_branchlength(self,root=None,node=None)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="set_subtree"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">set_subtree</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">node</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.set_subtree">source code</a></span>
</td>
</tr></table>
<p>Return subtree as a set of nested sets.</p>
<p>sets = set_subtree(self,node)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="is_identical"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">is_identical</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">tree2</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_identical">source code</a></span>
</td>
</tr></table>
<p>Compare tree and tree2 for identity.</p>
<p>result = is_identical(self,tree2)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="is_compatible"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">is_compatible</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">tree2</span>,
<span class="sig-arg">threshold</span>,
<span class="sig-arg">strict</span>=<span class="sig-default">True</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_compatible">source code</a></span>
</td>
</tr></table>
<p>Compares branches with support>threshold for compatibility.</p>
<p>result = is_compatible(self,tree2,threshold)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="common_ancestor"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">common_ancestor</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">node1</span>,
<span class="sig-arg">node2</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.common_ancestor">source code</a></span>
</td>
</tr></table>
<p>Return the common ancestor that connects two nodes.</p>
<p>node_id = common_ancestor(self,node1,node2)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="distance"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">distance</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">node1</span>,
<span class="sig-arg">node2</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.distance">source code</a></span>
</td>
</tr></table>
<p>Add and return the sum of the branchlengths between two nodes. dist =
distance(self,node1,node2)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="is_monophyletic"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">is_monophyletic</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">taxon_list</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_monophyletic">source code</a></span>
</td>
</tr></table>
<p>Return node_id of common ancestor if taxon_list is monophyletic, -1
otherwise.</p>
<p>result = is_monophyletic(self,taxon_list)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="branchlength2support"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">branchlength2support</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.branchlength2support">source code</a></span>
</td>
</tr></table>
<p>Move values stored in data.branchlength to data.support, and set
branchlength to 0.0</p>
<p>This is necessary when support has been stored as branchlength (e.g.
paup), and has thus been read in as branchlength.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="convert_absolute_support"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">convert_absolute_support</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">nrep</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.convert_absolute_support">source code</a></span>
</td>
</tr></table>
<p>Convert absolute support (clade-count) to rel. frequencies.</p>
<p>Some software (e.g. PHYLIP consense) just calculate how often clades
appear, instead of calculating relative frequencies.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="randomize"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">randomize</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">ntax</span>=<span class="sig-default">None</span>,
<span class="sig-arg">taxon_list</span>=<span class="sig-default">None</span>,
<span class="sig-arg">branchlength</span>=<span class="sig-default">1.0</span>,
<span class="sig-arg">branchlength_sd</span>=<span class="sig-default">None</span>,
<span class="sig-arg">bifurcate</span>=<span class="sig-default">True</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.randomize">source code</a></span>
</td>
</tr></table>
<p>Generates a random tree with ntax taxa and/or taxa from taxlabels.</p>
<p>new_tree =
randomize(self,ntax=None,taxon_list=None,branchlength=1.0,branchlength_sd=None,bifurcate=True)
Trees are bifurcating by default. (Polytomies not yet supported).</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="to_string"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">to_string</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">support_as_branchlengths</span>=<span class="sig-default">False</span>,
<span class="sig-arg">branchlengths_only</span>=<span class="sig-default">False</span>,
<span class="sig-arg">plain</span>=<span class="sig-default">True</span>,
<span class="sig-arg">plain_newick</span>=<span class="sig-default">False</span>,
<span class="sig-arg">ladderize</span>=<span class="sig-default">None</span>,
<span class="sig-arg">ignore_comments</span>=<span class="sig-default">True</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.to_string">source code</a></span>
</td>
</tr></table>
<p>Return a paup compatible tree line.</p>
<p>to_string(self,support_as_branchlengths=False,branchlengths_only=False,plain=True)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="__str__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__str__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Informal representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.__str__">source code</a></span>
</td>
</tr></table>
<p>Short version of to_string(), gives plain tree</p>
<dl class="fields">
<dt>Overrides:
object.__str__
</dt>
</dl>
</td></tr></table>
</div>
<a name="merge_with_support"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">merge_with_support</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">bstrees</span>=<span class="sig-default">None</span>,
<span class="sig-arg">constree</span>=<span class="sig-default">None</span>,
<span class="sig-arg">threshold</span>=<span class="sig-default">0.5</span>,
<span class="sig-arg">outgroup</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.merge_with_support">source code</a></span>
</td>
</tr></table>
<p>Merges clade support (from consensus or list of bootstrap-trees) with
phylogeny.</p>
<p>tree=merge_bootstrap(phylo,bs_tree=<list_of_trees>) or
tree=merge_bootstrap(phylo,consree=consensus_tree with clade support)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
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