Automated update e763ca5721d9c02d7ed7948e62299ae264076fce

Author: Sphinx

dev/Tutorial/chapter_phylo.html

@@ -66,6 +66,8 @@
 <li class="toctree-l2 current"><a class="current reference internal" href="#">Phylogenetics with Bio.Phylo</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#demo-whats-in-a-tree">Demo: What’s in a Tree?</a><ul>
 <li class="toctree-l4"><a class="reference internal" href="#coloring-branches-within-a-tree">Coloring branches within a tree</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#drawing-trees-with-iplotx">Drawing trees with iplotx</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#writing-tree-to-file">Writing tree to file</a></li>
 </ul>
 </li>
 <li class="toctree-l3"><a class="reference internal" href="#i-o-functions">I/O functions</a></li>
@@ -299,6 +301,29 @@ <h3>Coloring branches within a tree<a class="headerlink" href="#coloring-branche
 well as its descendents. The common ancestor of E and F turns out to be
 just under the root, and with this coloring we can see exactly where the
 root of the tree is.</p>
+</section>
+<section id="drawing-trees-with-iplotx">
+<h3>Drawing trees with iplotx<a class="headerlink" href="#drawing-trees-with-iplotx" title="Link to this heading"></a></h3>
+<p>For users seeking advanced styling options, Bio.Phylo trees are natively
+supported by the external library <code class="docutils literal notranslate"><span class="pre">iplotx</span></code>:</p>
+<p><a class="reference external" href="https://iplotx.readthedocs.io/en/latest/">https://iplotx.readthedocs.io/en/latest/</a></p>
+<p><code class="docutils literal notranslate"><span class="pre">iplotx</span></code> enables customisation of many aspects of the visualisation,
+including layout, vertex and branch properties, cascading backgrounds,
+and labels. Here is a self-contained example.</p>
+<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio</span><span class="w"> </span><span class="kn">import</span> <span class="n">Phylo</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span><span class="w"> </span><span class="nn">iplotx</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">ipx</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">tree</span> <span class="o">=</span> <span class="n">Phylo</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="s2">&quot;simple.dnd&quot;</span><span class="p">,</span> <span class="s2">&quot;newick&quot;</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">ipx</span><span class="o">.</span><span class="n">tree</span><span class="p">(</span><span class="n">tree</span><span class="p">,</span> <span class="n">leaf_deep</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">leaf_labels</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">style</span><span class="o">=</span><span class="s2">&quot;tree&quot;</span><span class="p">)</span>
+</pre></div>
+</div>
+<figure class="align-default" id="fig-phylo-color-iplotx">
+<a class="reference internal image-reference" href="../_images/phylo-color-iplotx.png"><img alt="A colorized tree drawn with ``iplotx.tree``." src="../_images/phylo-color-iplotx.png" style="width: 70.0%;" />
+</a>
+</figure>
+<p><code class="docutils literal notranslate"><span class="pre">iplotx</span></code> has an extensive <a class="reference external" href="https://iplotx.readthedocs.io/en/latest/gallery/index.html">gallery of examples</a>.</p>
+</section>
+<section id="writing-tree-to-file">
+<h3>Writing tree to file<a class="headerlink" href="#writing-tree-to-file" title="Link to this heading"></a></h3>
 <p>My, we’ve accomplished a lot! Let’s take a break here and save our work.
 Call the <code class="docutils literal notranslate"><span class="pre">write</span></code> function with a file name or handle — here we use
 standard output, to see what would be written — and the format