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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Phylo-module.html">Package Phylo</a> ::
<a href="Bio.Phylo.PhyloXML-module.html">Module PhyloXML</a> ::
Class Phylogeny
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Phylogeny</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Phylogeny">source code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="Bio.Phylo.BaseTree.TreeElement-class.html">BaseTree.TreeElement</a> --+
|
<a href="Bio.Phylo.PhyloXML.PhyloElement-class.html">PhyloElement</a> --+
|
object --+ |
| |
<a href="Bio.Phylo.BaseTree.TreeElement-class.html">BaseTree.TreeElement</a> --+ |
| |
object --+ | |
| | |
<a href="Bio.Phylo.BaseTree.TreeMixin-class.html">BaseTree.TreeMixin</a> --+ |
| |
<a href="Bio.Phylo.BaseTree.Tree-class.html">BaseTree.Tree</a> --+
|
<strong class="uidshort">Phylogeny</strong>
</pre>
<hr />
A phylogenetic tree.
<!-- ==================== 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.Phylo.PhyloXML.Phylogeny-class.html#__init__" class="summary-sig-name">__init__</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">rooted</span>=<span class="summary-sig-default">True</span>,
<span class="summary-sig-arg">rerootable</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">branch_length_unit</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">type</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">name</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">description</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">date</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">confidences</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">clade_relations</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">sequence_relations</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">properties</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">other</span>=<span class="summary-sig-default">None</span>)</span><br />
x.__init__(...) initializes x; see help(type(x)) for signature</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Phylogeny.__init__">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.Phylo.PhyloXML.Phylogeny-class.html#as_phyloxml" class="summary-sig-name">as_phyloxml</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return this tree, a PhyloXML-compatible Phylogeny object.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Phylogeny.as_phyloxml">source code</a></span>
</td>
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</table>
</td>
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<tr>
<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 name="to_phyloxml_container"></a><span class="summary-sig-name">to_phyloxml_container</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">**kwargs</span>)</span><br />
Create a new Phyloxml object containing just this phylogeny.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Phylogeny.to_phyloxml_container">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="to_alignment"></a><span class="summary-sig-name">to_alignment</span>(<span class="summary-sig-arg">self</span>)</span><br />
Construct an alignment from the aligned sequences in this tree.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Phylogeny.to_alignment">source code</a></span>
</td>
</tr>
</table>
</td>
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<tr class="private">
<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.Phylo.PhyloXML.Phylogeny-class.html#_get_confidence" class="summary-sig-name" onclick="show_private();">_get_confidence</a>(<span class="summary-sig-arg">self</span>)</span><br />
Equivalent to self.confidences[0] if there is only 1 value.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Phylogeny._get_confidence">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_set_confidence"></a><span class="summary-sig-name">_set_confidence</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Phylogeny._set_confidence">source code</a></span>
</td>
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</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 name="_del_confidence"></a><span class="summary-sig-name">_del_confidence</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Phylogeny._del_confidence">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.Phylo.BaseTree.Tree-class.html">BaseTree.Tree</a></code></b>:
<code><a href="Bio.Phylo.BaseTree.Tree-class.html#__format__">__format__</a></code>,
<code><a href="Bio.Phylo.BaseTree.Tree-class.html#__str__">__str__</a></code>,
<code><a href="Bio.Phylo.BaseTree.Tree-class.html#format">format</a></code>,
<code><a href="Bio.Phylo.BaseTree.Tree-class.html#is_terminal">is_terminal</a></code>,
<code><a href="Bio.Phylo.BaseTree.Tree-class.html#root_with_outgroup">root_with_outgroup</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Phylo.BaseTree.TreeElement-class.html">BaseTree.TreeElement</a></code></b>:
<code><a href="Bio.Phylo.BaseTree.TreeElement-class.html#__repr__">__repr__</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html">BaseTree.TreeMixin</a></code></b>:
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#collapse">collapse</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#collapse_all">collapse_all</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#common_ancestor">common_ancestor</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#count_terminals">count_terminals</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#depths">depths</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#distance">distance</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#find_any">find_any</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#find_clades">find_clades</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#find_elements">find_elements</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#get_nonterminals">get_nonterminals</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#get_path">get_path</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#get_terminals">get_terminals</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#is_bifurcating">is_bifurcating</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#is_monophyletic">is_monophyletic</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#is_parent_of">is_parent_of</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#is_preterminal">is_preterminal</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#ladderize">ladderize</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#prune">prune</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#split">split</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#total_branch_length">total_branch_length</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#trace">trace</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html">BaseTree.TreeMixin</a></code></b> (private):
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#_filter_search" onclick="show_private();">_filter_search</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
</p>
</td>
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<!-- ==================== CLASS METHODS ==================== -->
<a name="section-ClassMethods"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<td align="left"><span class="table-header">Class Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-ClassMethods"
class="privatelink" onclick="toggle_private();"
>hide private</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">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Phylo.PhyloXML.Phylogeny-class.html#from_tree" class="summary-sig-name">from_tree</a>(<span class="summary-sig-arg">cls</span>,
<span class="summary-sig-arg">tree</span>,
<span class="summary-sig-arg">**kwargs</span>)</span><br />
Create a new Phylogeny given a Tree (from Newick/Nexus or BaseTree).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Phylogeny.from_tree">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.Phylo.PhyloXML.Phylogeny-class.html#from_clade" class="summary-sig-name">from_clade</a>(<span class="summary-sig-arg">cls</span>,
<span class="summary-sig-arg">clade</span>,
<span class="summary-sig-arg">**kwargs</span>)</span><br />
Create a new Phylogeny given a Newick or BaseTree Clade object.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Phylogeny.from_clade">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.Phylo.BaseTree.Tree-class.html">BaseTree.Tree</a></code></b>:
<code><a href="Bio.Phylo.BaseTree.Tree-class.html#randomized">randomized</a></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 width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Phylo.PhyloXML.Phylogeny-class.html#confidence" class="summary-name">confidence</a><br />
Equivalent to self.confidences[0] if there is only 1 value.
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Phylo.BaseTree.Tree-class.html">BaseTree.Tree</a></code></b>:
<code><a href="Bio.Phylo.BaseTree.Tree-class.html#clade">clade</a></code>
</p>
<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"
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<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>
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<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">root</span>=<span class="sig-default">None</span>,
<span class="sig-arg">rooted</span>=<span class="sig-default">True</span>,
<span class="sig-arg">rerootable</span>=<span class="sig-default">None</span>,
<span class="sig-arg">branch_length_unit</span>=<span class="sig-default">None</span>,
<span class="sig-arg">type</span>=<span class="sig-default">None</span>,
<span class="sig-arg">name</span>=<span class="sig-default">None</span>,
<span class="sig-arg">id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">description</span>=<span class="sig-default">None</span>,
<span class="sig-arg">date</span>=<span class="sig-default">None</span>,
<span class="sig-arg">confidences</span>=<span class="sig-default">None</span>,
<span class="sig-arg">clade_relations</span>=<span class="sig-default">None</span>,
<span class="sig-arg">sequence_relations</span>=<span class="sig-default">None</span>,
<span class="sig-arg">properties</span>=<span class="sig-default">None</span>,
<span class="sig-arg">other</span>=<span class="sig-default">None</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Phylogeny.__init__">source code</a></span>
</td>
</tr></table>
<p>x.__init__(...) initializes x; see help(type(x)) for signature</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>root</code></strong> (Clade) - the root node/clade of this tree</li>
<li><strong class="pname"><code>rooted</code></strong> (bool) - True if this tree is rooted</li>
<li><strong class="pname"><code>rerootable</code></strong> (bool) - True if this tree is rerootable</li>
<li><strong class="pname"><code>branch_length_unit</code></strong> (string) - unit for branch_length values on clades</li>
<li><strong class="pname"><code>name</code></strong> (string) - identifier for this tree, not required to be unique</li>
<li><strong class="pname"><code>id</code></strong> (Id) - unique identifier for this tree</li>
<li><strong class="pname"><code>description</code></strong> (string) - plain-text description</li>
<li><strong class="pname"><code>date</code></strong> (Date) - date for the root node of this tree</li>
<li><strong class="pname"><code>confidences</code></strong> (list) - Confidence objects for this tree</li>
<li><strong class="pname"><code>clade_relations</code></strong> (list) - CladeRelation objects</li>
<li><strong class="pname"><code>sequence_relations</code></strong> (list) - SequenceRelation objects</li>
<li><strong class="pname"><code>properties</code></strong> (list) - Property objects</li>
<li><strong class="pname"><code>other</code></strong> (list) - non-phyloXML elements (type <a href="Bio.Phylo.PhyloXML.Other-class.html" class="link">Other</a>)</li>
</ul></dd>
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="from_tree"></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">from_tree</span>(<span class="sig-arg">cls</span>,
<span class="sig-arg">tree</span>,
<span class="sig-arg">**kwargs</span>)</span>
<br /><em class="fname">Class Method</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Phylogeny.from_tree">source code</a></span>
</td>
</tr></table>
<p>Create a new Phylogeny given a Tree (from Newick/Nexus or BaseTree).</p>
<p>Keyword arguments are the usual <a href="Bio.Phylo.PhyloXML.Phylogeny-class.html" class="link">Phylogeny</a> constructor parameters.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="from_clade"></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">from_clade</span>(<span class="sig-arg">cls</span>,
<span class="sig-arg">clade</span>,
<span class="sig-arg">**kwargs</span>)</span>
<br /><em class="fname">Class Method</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Phylogeny.from_clade">source code</a></span>
</td>
</tr></table>
<p>Create a new Phylogeny given a Newick or BaseTree Clade object.</p>
<p>Keyword arguments are the usual <a href="Bio.Phylo.PhyloXML.Clade-class.html" class="link">PhyloXML.Clade</a> constructor parameters.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.Phylo.BaseTree.Tree-class.html#from_clade">BaseTree.Tree.from_clade</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="as_phyloxml"></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">as_phyloxml</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Phylogeny.as_phyloxml">source code</a></span>
</td>
</tr></table>
<p>Return this tree, a PhyloXML-compatible Phylogeny object.</p>
<p>Overrides the <a href="Bio.Phylo.BaseTree-module.html" class="link">BaseTree</a> method.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.Phylo.BaseTree.Tree-class.html#as_phyloxml">BaseTree.Tree.as_phyloxml</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="_get_confidence"></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">_get_confidence</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Phylogeny._get_confidence">source code</a></span>
</td>
</tr></table>
<p>Equivalent to self.confidences[0] if there is only 1 value.</p>
<p>See also: <a href="Bio.Phylo.PhyloXML.Clade-class.html#confidence" class="link">Clade.confidence</a>, <a href="Bio.Phylo.PhyloXML.Clade-class.html#taxonomy" class="link">Clade.taxonomy</a></p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== PROPERTY DETAILS ==================== -->
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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">Property Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-PropertyDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
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</td>
</tr>
</table>
<a name="confidence"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">confidence</h3>
<p>Equivalent to self.confidences[0] if there is only 1 value.</p>
<p>See also: <a href="Bio.Phylo.PhyloXML.Clade-class.html#confidence" class="link">Clade.confidence</a>, <a href="Bio.Phylo.PhyloXML.Clade-class.html#taxonomy" class="link">Clade.taxonomy</a></p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="Bio.Phylo.PhyloXML.Phylogeny-class.html#_get_confidence" class="summary-sig-name" onclick="show_private();">_get_confidence</a>(<span class="summary-sig-arg">self</span>)</span>
- Equivalent to self.confidences[0] if there is only 1 value.
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><a href="Bio.Phylo.PhyloXML.Phylogeny-class.html#_set_confidence" class="summary-sig-name" onclick="show_private();">_set_confidence</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span>
</dd>
<dt>Delete Method:</dt>
<dd class="value"><span class="summary-sig"><a href="Bio.Phylo.PhyloXML.Phylogeny-class.html#_del_confidence" class="summary-sig-name" onclick="show_private();">_del_confidence</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
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