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‎_sources/reference/reference_tree.rst.txt‎

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Tree (main class)
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=================
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.. autoclass:: ete4.Tree
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.. automodule:: ete4.core.tree
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:members:
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:undoc-members:
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:special-members: __init__

‎_sources/tutorial/tutorial_trees.rst.txt‎

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node names. Nevertheless, it is not uncommon to find slightly
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different variations of the format.
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ETE can read and write many of them:
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ETE can read and write many of them (normally with ``Tree(...,
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parser=...)``, see :ref:`sec:reading-newick`):
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.. table::
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====== ========================================= =============================================
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Format Description Example
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====== ========================================= =============================================
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0 internal nodes with support (flexible) ((D:0.7,F:0.5)1.0:0.6,(B:0.2,H:0.7)1.0:0.8);
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1 internal nodes with names (flexible) ((D:0.7,F:0.5)E:0.6,(B:0.2,H:0.7)B:0.8);
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2 internal w/ support, all lengths present ((D:0.7,F:0.5)1.0:0.6,(B:0.2,H:0.7)1.0:0.8);
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3 internal w/ names, all lengths present ((D:0.7,F:0.5)E:0.6,(B:0.2,H:0.7)B:0.8);
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4 names and lengths for leaves only ((D:0.7,F:0.5),(B:0.2,H:0.7));
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5 leaf names and all lengths ((D:0.7,F:0.5):0.6,(B:0.2,H:0.7):0.8);
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6 leaf names and internal lengths ((D,F):0.6,(B,H):0.8);
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7 all names and leaf lengths ((D:0.7,F:0.5)E,(B:0.2,H:0.7)B);
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8 all names (leaves and internal nodes) ((D,F)E,(B,H)B);
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9 leaf names only ((D,F),(B,H));
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100 topology only ((,),(,));
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====== ========================================= =============================================
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====== ======================================== =================================
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Format Description Example
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====== ======================================== =================================
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0 (*) internal nodes with support (flexible) ((D:2,E:5)1.0:9,(F:6,G):7);
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1 internal nodes with names (flexible) ((D:2,E:5)B:9,(F:6,G):7);
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2 internal w/ support, all values present ((D:2,E:5)1.0:9,(F:6,G:3)1.0:7);
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3 internal w/ names, all values present ((D:2,E:5)B:9,(F:6,G:3)C:7);
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4 names and lengths for leaves only ((D:2,E:5),(F:6,G:3));
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5 leaf names and all lengths ((D:2,E:5):9,(F:6,G:3):7);
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6 leaf names and internal lengths ((D,F):6,(B,H):8);
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7 all names and leaf lengths ((D:2,E:5)B,(F:6,G:3)C);
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8 all names (leaves and internal nodes) ((D,E)B,(F,G)C);
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9 leaf names only ((D,E),(F,G));
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100 topology only ((,),(,));
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====== ======================================== =================================
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where the example tree would look (more or less) like::
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╭╴D:2
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╭╴B:9╶┤
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│ ╰╴E:5
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╶┤
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│ ╭╴F:6
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╰╴C:7╶┤
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╰╴G:3
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Formats labeled as *flexible* allow for missing information. For
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instance, format 0 will be able to load a newick tree even if it does
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# ╰╴j
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.. _sec:reading-newick:
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Reading newick trees
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~~~~~~~~~~~~~~~~~~~~
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‎genindex.html‎

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‎internals/internals_essentials.html‎

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evolutionary distance between the nodes, and other <em>branch
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properties</em>.</p>
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<img alt="../_images/tree.png" src="../_images/tree.png" />
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<p>In the representation that we have chosen, a <a class="reference internal" href="../reference/reference_tree.html#ete4.Tree" title="ete4.Tree"><code class="xref py py-class docutils literal notranslate"><span class="pre">Tree</span></code></a> is a
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<p>In the representation that we have chosen, a <code class="xref py py-class docutils literal notranslate"><span class="pre">Tree</span></code> is a
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structure with some content (internally stored in a dictionary
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<code class="docutils literal notranslate"><span class="pre">props</span></code> of properties) and a list of <code class="docutils literal notranslate"><span class="pre">children</span></code>, which can be
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viewed as trees themselves. It can have a parent (<code class="docutils literal notranslate"><span class="pre">up</span></code>), which is
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</section>
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<section id="size">
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<h2>Size<a class="headerlink" href="#size" title="Link to this heading"></a></h2>
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<p>A <a class="reference internal" href="../reference/reference_tree.html#ete4.Tree" title="ete4.Tree"><code class="xref py py-class docutils literal notranslate"><span class="pre">Tree</span></code></a> also has a <code class="docutils literal notranslate"><span class="pre">size</span></code>, which is a tuple <code class="docutils literal notranslate"><span class="pre">(dx,</span> <span class="pre">dy)</span></code>
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<p>A <code class="xref py py-class docutils literal notranslate"><span class="pre">Tree</span></code> also has a <code class="docutils literal notranslate"><span class="pre">size</span></code>, which is a tuple <code class="docutils literal notranslate"><span class="pre">(dx,</span> <span class="pre">dy)</span></code>
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formed by the distance to its further leaf (including its own length),
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and the total number of descendant leaves.</p>
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<p>This concept is exploited when drawing with different representations,

‎objects.inv‎

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‎py-modindex.html‎

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<td>&#160;&#160;&#160;
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<a href="reference/reference_seqgroup.html#module-ete4.core.seqgroup"><code class="xref">ete4.core.seqgroup</code></a></td><td>
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<em></em></td></tr>
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<tr class="cg-1">
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<td></td>
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<td>&#160;&#160;&#160;
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<a href="reference/reference_tree.html#module-ete4.core.tree"><code class="xref">ete4.core.tree</code></a></td><td>
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<em></em></td></tr>
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<tr class="cg-1">
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<td></td>
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<td>&#160;&#160;&#160;

‎reference/index.html‎

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<div class="toctree-wrapper compound">
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="reference_tree.html">Tree (main class)</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="reference_tree.html#ete4.Tree"><code class="docutils literal notranslate"><span class="pre">Tree</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="reference_tree.html#ete4.core.tree.Tree"><code class="docutils literal notranslate"><span class="pre">Tree</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="reference_tree.html#ete4.core.tree.TreeError"><code class="docutils literal notranslate"><span class="pre">TreeError</span></code></a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="reference_operations.html">Tree operations</a><ul>

‎reference/reference_parsers.html‎

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<section id="module-ete4.parser.newick">
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<span id="newick"></span><h2>Newick<a class="headerlink" href="#module-ete4.parser.newick" title="Link to this heading"></a></h2>
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<p>Parser for trees represented in newick format.</p>
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<p>The main functions are <code class="docutils literal notranslate"><span class="pre">loads()</span></code> and <code class="docutils literal notranslate"><span class="pre">dumps()</span></code>, which read/write a tree
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from/to its newick text representation.</p>
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<p>When reading a newick file, the argument <code class="docutils literal notranslate"><span class="pre">parser=...</span></code> specifies
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which kind of parser to use.</p>
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<p>The classical ones in ete are the following:</p>
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<table class="docutils align-default">
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<thead>
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<tr class="row-odd"><th class="head"><p>Format</p></th>
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<th class="head"><p>Description</p></th>
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<th class="head"><p>Example</p></th>
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</tr>
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</thead>
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<tbody>
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<tr class="row-even"><td><p>0 (*)</p></td>
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<td><p>internal nodes with support (flexible)</p></td>
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<td><p>((D:2,E:5)1.0:9,(F:6,G):7);</p></td>
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</tr>
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<tr class="row-odd"><td><p>1</p></td>
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<td><p>internal nodes with names (flexible)</p></td>
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<td><p>((D:2,E:5)B:9,(F:6,G):7);</p></td>
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</tr>
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<tr class="row-even"><td><p>2</p></td>
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<td><p>internal w/ support, all values present</p></td>
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<td><p>((D:2,E:5)1.0:9,(F:6,G:3)1.0:7);</p></td>
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</tr>
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<tr class="row-odd"><td><p>3</p></td>
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<td><p>internal w/ names, all values present</p></td>
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<td><p>((D:2,E:5)B:9,(F:6,G:3)C:7);</p></td>
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</tr>
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<tr class="row-even"><td><p>4</p></td>
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<td><p>names and lengths for leaves only</p></td>
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<td><p>((D:2,E:5),(F:6,G:3));</p></td>
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</tr>
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<tr class="row-odd"><td><p>5</p></td>
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<td><p>leaf names and all lengths</p></td>
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<td><p>((D:2,E:5):9,(F:6,G:3):7);</p></td>
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</tr>
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<tr class="row-even"><td><p>6</p></td>
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<td><p>leaf names and internal lengths</p></td>
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<td><p>((D,F):6,(B,H):8);</p></td>
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</tr>
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<tr class="row-odd"><td><p>7</p></td>
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<td><p>all names and leaf lengths</p></td>
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<td><p>((D:2,E:5)B,(F:6,G:3)C);</p></td>
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</tr>
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<tr class="row-even"><td><p>8</p></td>
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<td><p>all names (leaves and internal nodes)</p></td>
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<td><p>((D,E)B,(F,G)C);</p></td>
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</tr>
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<tr class="row-odd"><td><p>9</p></td>
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<td><p>leaf names only</p></td>
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<td><p>((D,E),(F,G));</p></td>
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</tr>
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<tr class="row-even"><td><p>100</p></td>
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<td><p>topology only</p></td>
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<td><p>((,),(,));</p></td>
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</tr>
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</tbody>
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</table>
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<p>where the example tree would look (more or less) like:</p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span> ╭╴D:2
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╭╴B:9╶┤
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│ ╰╴E:5
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╶┤
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│ ╭╴F:6
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╰╴C:7╶┤
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╰╴G:3
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</pre></div>
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</div>
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<p>There are other valid values for <code class="docutils literal notranslate"><span class="pre">parser</span></code>:</p>
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<ul class="simple">
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<li><p><code class="docutils literal notranslate"><span class="pre">'name'</span></code>, same as 1</p></li>
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<li><p><code class="docutils literal notranslate"><span class="pre">'support'</span></code>, same as 0</p></li>
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<li><p><code class="docutils literal notranslate"><span class="pre">'multisupport'</span></code>, internal nodes look like <code class="docutils literal notranslate"><span class="pre">((X:5)80/100:7)...</span></code>, that is,
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have multiple values of support separated by <code class="docutils literal notranslate"><span class="pre">/</span></code></p></li>
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</ul>
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<p>More generally, <code class="docutils literal notranslate"><span class="pre">parser</span></code> can be a dictionary that specifies in
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detail how to read/write each field. It must say, for leaf and internal
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nodes, what <code class="docutils literal notranslate"><span class="pre">p0:p1</span></code> means (which properties they are, including how
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to read and write them). For example, the default parser looks like:</p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">PARSER_DEFAULT</span> <span class="o">=</span> <span class="p">{</span>
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<span class="s1">&#39;leaf&#39;</span><span class="p">:</span> <span class="p">[</span><span class="n">NAME</span><span class="p">,</span> <span class="n">DIST</span><span class="p">],</span> <span class="c1"># ((name:dist)x:y);</span>
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<span class="s1">&#39;internal&#39;</span><span class="p">:</span> <span class="p">[</span><span class="n">SUPPORT</span><span class="p">,</span> <span class="n">DIST</span><span class="p">],</span> <span class="c1"># ((x:y)support:dist);</span>
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<span class="p">}</span>
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</pre></div>
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</div>
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<p>where <code class="docutils literal notranslate"><span class="pre">NAME</span></code> and <code class="docutils literal notranslate"><span class="pre">DIST</span></code> are “property dicts”, that have all the
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information for a property (<code class="docutils literal notranslate"><span class="pre">pname</span></code>) to know which function to apply
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to read/write from/to a string. For example, <code class="docutils literal notranslate"><span class="pre">DIST</span></code> is:</p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">DIST</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;pname&#39;</span><span class="p">:</span> <span class="s1">&#39;dist&#39;</span><span class="p">,</span> <span class="s1">&#39;read&#39;</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span> <span class="s1">&#39;write&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="s1">&#39;</span><span class="si">%g</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">float</span><span class="p">(</span><span class="n">x</span><span class="p">)}</span>
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</pre></div>
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</div>
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<dl class="py exception">
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<dt class="sig sig-object py" id="ete4.parser.newick.NewickError">
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<em class="property"><span class="k"><span class="pre">exception</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">NewickError</span></span><a class="headerlink" href="#ete4.parser.newick.NewickError" title="Link to this definition"></a></dt>

‎reference/reference_phylo.html‎

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<dl class="py class">
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<dt class="sig sig-object py" id="ete4.PhyloTree">
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<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PhyloTree</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">newick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">children</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alignment</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alg_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'fasta'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sp_naming_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parser</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/ete4/phylo/phylotree.html#PhyloTree"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ete4.PhyloTree" title="Link to this definition"></a></dt>
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<dd><p>Bases: <a class="reference internal" href="reference_tree.html#ete4.Tree" title="ete4.core.tree.Tree"><code class="xref py py-class docutils literal notranslate"><span class="pre">Tree</span></code></a></p>
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<dd><p>Bases: <a class="reference internal" href="reference_tree.html#ete4.core.tree.Tree" title="ete4.core.tree.Tree"><code class="xref py py-class docutils literal notranslate"><span class="pre">Tree</span></code></a></p>
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<p>Class to store a phylogenetic tree.</p>
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<p>Extends the standard <a class="reference internal" href="reference_tree.html#ete4.Tree" title="ete4.Tree"><code class="xref py py-class docutils literal notranslate"><span class="pre">Tree</span></code></a> instance by adding
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<p>Extends the standard <code class="xref py py-class docutils literal notranslate"><span class="pre">Tree</span></code> instance by adding
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specific properties and methods to work with phylogentic trees.</p>
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<dl class="py method">
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<dt class="sig sig-object py" id="ete4.PhyloTree.__init__">

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