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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 68b3ac557283062eecaf4575981a5559
+config: afc012072ef80725e8359fbfe2cd543a
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_modules/ete4/clustering/clustertree.html b/_modules/ete4/clustering/clustertree.html
@@ -7,7 +7,6 @@
     <title>ete4.clustering.clustertree &#8212; ETE Toolkit 4.0.0-beta documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=4f649999" />
     <link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css?v=039e1c02" />
-    <link rel="stylesheet" type="text/css" href="../../../_static/graphviz.css?v=eafc0fe6" />
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     <script src="../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>

diff --git a/_modules/ete4/coretype/seqgroup.html b/_modules/ete4/coretype/seqgroup.html
@@ -7,7 +7,6 @@
     <title>ete4.coretype.seqgroup &#8212; ETE Toolkit 4.0.0-beta documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=4f649999" />
     <link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css?v=039e1c02" />
-    <link rel="stylesheet" type="text/css" href="../../../_static/graphviz.css?v=eafc0fe6" />
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     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
@@ -57,7 +56,7 @@ <h1>Source code for ete4.coretype.seqgroup</h1><div class="highlight"><pre>
 <a class="viewcode-back" href="../../../reference/reference_seqgroup.html#ete4.coretype.seqgroup.SeqGroup.__init__">[docs]</a>
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sequences</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="s1">&#39;fasta&#39;</span><span class="p">,</span>
                  <span class="n">fix_duplicates</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="w">        </span><span class="sa">r</span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        :param sequences: Path to the file containing the sequences or,</span>
 <span class="sd">            alternatively, the text string containing them.</span>
 <span class="sd">        :param format: Encoding format of sequences. Supported formats</span>
@@ -69,9 +68,12 @@ <h1>Source code for ete4.coretype.seqgroup</h1><div class="highlight"><pre>
 
 <span class="sd">        Example::</span>
 
-<span class="sd">          msf = &#39;&gt;seq1\\nAAAAAAAAAAA\\n&gt;seq2\\nTTTTTTTTTTTTT\\n&#39;</span>
-<span class="sd">          seqs = SeqGroup(msf, format=&#39;fasta&#39;)</span>
-<span class="sd">          print seqs.get_seq(&#39;seq1&#39;)</span>
+<span class="sd">          seqs_str = (&#39;&gt;seq1\n&#39;</span>
+<span class="sd">                      &#39;AAAAAAAAAAA\n&#39;</span>
+<span class="sd">                      &#39;&gt;seq2\n&#39;</span>
+<span class="sd">                      &#39;TTTTTTTTTTTTT\n&#39;)</span>
+<span class="sd">          seqs = SeqGroup(seqs_str, format=&#39;fasta&#39;)</span>
+<span class="sd">          print(seqs.get_seq(&#39;seq1&#39;))</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">parsers</span> <span class="o">=</span> <span class="p">{</span>
             <span class="s1">&#39;fasta&#39;</span><span class="p">:</span> <span class="p">[</span><span class="n">read_fasta</span><span class="p">,</span> <span class="n">write_fasta</span><span class="p">,</span> <span class="p">{}],</span>

diff --git a/_modules/ete4/ncbi_taxonomy/ncbiquery.html b/_modules/ete4/ncbi_taxonomy/ncbiquery.html
@@ -7,7 +7,6 @@
     <title>ete4.ncbi_taxonomy.ncbiquery &#8212; ETE Toolkit 4.0.0-beta documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=4f649999" />
     <link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css?v=039e1c02" />
-    <link rel="stylesheet" type="text/css" href="../../../_static/graphviz.css?v=eafc0fe6" />
     <script src="../../../_static/documentation_options.js?v=f03ed5e5"></script>
     <script src="../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>

diff --git a/_modules/ete4/phylo/evolevents.html b/_modules/ete4/phylo/evolevents.html
@@ -7,7 +7,6 @@
     <title>ete4.phylo.evolevents &#8212; ETE Toolkit 4.0.0-beta documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=4f649999" />
     <link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css?v=039e1c02" />
-    <link rel="stylesheet" type="text/css" href="../../../_static/graphviz.css?v=eafc0fe6" />
     <script src="../../../_static/documentation_options.js?v=f03ed5e5"></script>
     <script src="../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>

diff --git a/_modules/ete4/phylo/phylotree.html b/_modules/ete4/phylo/phylotree.html
@@ -7,7 +7,6 @@
     <title>ete4.phylo.phylotree &#8212; ETE Toolkit 4.0.0-beta documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=4f649999" />
     <link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css?v=039e1c02" />
-    <link rel="stylesheet" type="text/css" href="../../../_static/graphviz.css?v=eafc0fe6" />
     <script src="../../../_static/documentation_options.js?v=f03ed5e5"></script>
     <script src="../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
@@ -307,12 +306,15 @@ <h1>Source code for ete4.phylo.phylotree</h1><div class="highlight"><pre>
 <span class="sd">    specific properties and methods to work with phylogentic trees.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
+<div class="viewcode-block" id="PhyloTree.__init__">
+<a class="viewcode-back" href="../../../reference/reference_phylo.html#ete4.PhyloTree.__init__">[docs]</a>
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">newick</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">children</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">alignment</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
                  <span class="n">alg_format</span><span class="o">=</span><span class="s2">&quot;fasta&quot;</span><span class="p">,</span> <span class="n">sp_naming_function</span><span class="o">=</span><span class="n">_parse_species</span><span class="p">,</span>
                  <span class="n">parser</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">        :param newick: Path to the file containing the tree or, alternatively,</span>
-<span class="sd">            the text string containing the same information.</span>
+<span class="sd">        :param newick: If not None, initializes the tree from a newick,</span>
+<span class="sd">            which can be a string or file object containing it.</span>
+<span class="sd">        :param children: If not None, the children to add to this node.</span>
 <span class="sd">        :param alignment: File containing a multiple sequence alignment.</span>
 <span class="sd">        :param alg_format: &quot;fasta&quot;, &quot;phylip&quot; or &quot;iphylip&quot; (interleaved).</span>
 <span class="sd">        :param parser: Parser to read the newick.</span>
@@ -331,7 +333,8 @@ <h1>Source code for ete4.phylo.phylotree</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">link_to_alignment</span><span class="p">(</span><span class="n">alignment</span><span class="p">,</span> <span class="n">alg_format</span><span class="p">)</span>
 
         <span class="k">if</span> <span class="n">newick</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">set_species_naming_function</span><span class="p">(</span><span class="n">sp_naming_function</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">set_species_naming_function</span><span class="p">(</span><span class="n">sp_naming_function</span><span class="p">)</span></div>
+
 
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">species</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>

diff --git a/_modules/ete4/smartview/renderer/faces.html b/_modules/ete4/smartview/renderer/faces.html
@@ -7,7 +7,6 @@
     <title>ete4.smartview.renderer.faces &#8212; ETE Toolkit 4.0.0-beta documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=4f649999" />
     <link rel="stylesheet" type="text/css" href="../../../../_static/alabaster.css?v=039e1c02" />
-    <link rel="stylesheet" type="text/css" href="../../../../_static/graphviz.css?v=eafc0fe6" />
     <script src="../../../../_static/documentation_options.js?v=f03ed5e5"></script>
     <script src="../../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>

diff --git a/_modules/ete4/smartview/renderer/nodestyle.html b/_modules/ete4/smartview/renderer/nodestyle.html
@@ -7,7 +7,6 @@
     <title>ete4.smartview.renderer.nodestyle &#8212; ETE Toolkit 4.0.0-beta documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=4f649999" />
     <link rel="stylesheet" type="text/css" href="../../../../_static/alabaster.css?v=039e1c02" />
-    <link rel="stylesheet" type="text/css" href="../../../../_static/graphviz.css?v=eafc0fe6" />
     <script src="../../../../_static/documentation_options.js?v=f03ed5e5"></script>
     <script src="../../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>

diff --git a/_modules/ete4/smartview/renderer/treestyle.html b/_modules/ete4/smartview/renderer/treestyle.html
@@ -7,7 +7,6 @@
     <title>ete4.smartview.renderer.treestyle &#8212; ETE Toolkit 4.0.0-beta documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=4f649999" />
     <link rel="stylesheet" type="text/css" href="../../../../_static/alabaster.css?v=039e1c02" />
-    <link rel="stylesheet" type="text/css" href="../../../../_static/graphviz.css?v=eafc0fe6" />
     <script src="../../../../_static/documentation_options.js?v=f03ed5e5"></script>
     <script src="../../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>

diff --git a/_modules/index.html b/_modules/index.html
@@ -7,7 +7,6 @@
     <title>Overview: module code &#8212; ETE Toolkit 4.0.0-beta documentation</title>
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=4f649999" />
     <link rel="stylesheet" type="text/css" href="../_static/alabaster.css?v=039e1c02" />
-    <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
     <script src="../_static/documentation_options.js?v=f03ed5e5"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>

diff --git a/_sources/reference/index.rst.txt b/_sources/reference/index.rst.txt
@@ -1,20 +1,12 @@
 Reference Guide
 ===============
 
-.. inheritance-diagram::
-   ete4.coretype.tree
-   ete4.phylo.phylotree
-   ete4.clustering.clustertree
-   :parts: 1
-
-Current modules:
-
 .. toctree::
    :maxdepth: 2
 
    reference_tree
-   reference_treeview
    reference_phylo
    reference_clustering
    reference_seqgroup
+   reference_treeview
    reference_ncbi
diff --git a/_sources/reference/reference_phylo.rst.txt b/_sources/reference/reference_phylo.rst.txt
@@ -1,10 +1,12 @@
-PhyloTree class
-===============
+Phylogenetic trees
+==================
 
 .. autoclass:: ete4.PhyloTree
    :members:
    :undoc-members:
    :show-inheritance:
+   :special-members: __init__
 
 .. autoclass:: ete4.phylo.EvolEvent
    :members:
+   :undoc-members:
diff --git a/_sources/reference/reference_seqgroup.rst.txt b/_sources/reference/reference_seqgroup.rst.txt
@@ -1,5 +1,5 @@
-SeqGroup
-========
+Multiple Sequence Alignments (SeqGroup)
+=======================================
 
 .. automodule:: ete4.coretype.seqgroup
    :members:

diff --git a/_sources/reference/reference_tree.rst.txt b/_sources/reference/reference_tree.rst.txt
@@ -1,5 +1,5 @@
-Tree
-====
+Tree (main class)
+=================
 
 .. autoclass:: ete4.Tree
    :members:

diff --git a/_sources/reference/reference_treeview.rst.txt b/_sources/reference/reference_treeview.rst.txt
@@ -1,5 +1,5 @@
-Treeview
-========
+Treeview (graphics)
+===================
 
 .. contents::
 

diff --git a/_static/graphviz.css b/_static/graphviz.css
diff --git a/about.html b/about.html
@@ -8,7 +8,6 @@
     <title>About &#8212; ETE Toolkit 4.0.0-beta documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=4f649999" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=039e1c02" />
-    <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
     <script src="_static/documentation_options.js?v=f03ed5e5"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>

diff --git a/faqs.html b/faqs.html
@@ -8,7 +8,6 @@
     <title>Frequently Asked Questions (FAQs) &#8212; ETE Toolkit 4.0.0-beta documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=4f649999" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=039e1c02" />
-    <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
     <script src="_static/documentation_options.js?v=f03ed5e5"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>

diff --git a/genindex.html b/genindex.html
@@ -7,7 +7,6 @@
     <title>Index &#8212; ETE Toolkit 4.0.0-beta documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=4f649999" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=039e1c02" />
-    <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
     <script src="_static/documentation_options.js?v=f03ed5e5"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
@@ -62,6 +61,8 @@ <h2 id="_">_</h2>
 
       <ul>
         <li><a href="reference/reference_ncbi.html#ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.__init__">(NCBITaxa method)</a>
+</li>
+        <li><a href="reference/reference_phylo.html#ete4.PhyloTree.__init__">(PhyloTree method)</a>
 </li>
         <li><a href="reference/reference_seqgroup.html#ete4.coretype.seqgroup.SeqGroup.__init__">(SeqGroup method)</a>
 </li>

diff --git a/index.html b/index.html
@@ -8,7 +8,6 @@
     <title>Welcome to ETE’s documentation! &#8212; ETE Toolkit 4.0.0-beta documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=4f649999" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=039e1c02" />
-    <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
     <script src="_static/documentation_options.js?v=f03ed5e5"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
@@ -56,11 +55,11 @@ <h1>Welcome to ETE’s documentation!<a class="headerlink" href="#welcome-to-ete
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="reference/index.html">Reference Guide</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="reference/reference_tree.html">Tree</a></li>
-<li class="toctree-l2"><a class="reference internal" href="reference/reference_treeview.html">Treeview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="reference/reference_phylo.html">PhyloTree class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="reference/reference_tree.html">Tree (main class)</a></li>
+<li class="toctree-l2"><a class="reference internal" href="reference/reference_phylo.html">Phylogenetic trees</a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference/reference_clustering.html">Clustering</a></li>
-<li class="toctree-l2"><a class="reference internal" href="reference/reference_seqgroup.html">SeqGroup</a></li>
+<li class="toctree-l2"><a class="reference internal" href="reference/reference_seqgroup.html">Multiple Sequence Alignments (SeqGroup)</a></li>
+<li class="toctree-l2"><a class="reference internal" href="reference/reference_treeview.html">Treeview (graphics)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference/reference_ncbi.html">NCBITaxa</a></li>
 </ul>
 </li>

diff --git a/objects.inv b/objects.inv
diff --git a/py-modindex.html b/py-modindex.html
@@ -7,7 +7,6 @@
     <title>Python Module Index &#8212; ETE Toolkit 4.0.0-beta documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=4f649999" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=039e1c02" />
-    <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
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