From e89ea2ec6e4ff3b2c2100ebb3813f7e370776651 Mon Sep 17 00:00:00 2001
From: qiyunzhu <4396343+qiyunzhu@users.noreply.github.com>
Date: Fri, 30 Aug 2024 01:49:38 +0000
Subject: [PATCH] Update from
 https://github.com/scikit-bio/scikit-bio/commit/a8f9f9a5c045d0e2bb9046d0ab3e9557a36d59d3

---
 ....tree.TreeNode.accumulate_to_ancestor.html |  2 +-
 .../skbio.tree.TreeNode.ascii_art.html        |  2 +-
 .../skbio.tree.TreeNode.assign_ids.html       |  2 +-
 .../skbio.tree.TreeNode.assign_supports.html  |  2 +-
 .../skbio.tree.TreeNode.cache_attr.html       |  2 +-
 .../skbio.tree.TreeNode.clear_caches.html     |  2 +-
 .../skbio.tree.TreeNode.compare_rfd.html      |  2 +-
 .../skbio.tree.TreeNode.compare_subsets.html  |  2 +-
 ...o.tree.TreeNode.compare_tip_distances.html | 36 +++++------
 .../generated/skbio.tree.TreeNode.count.html  |  2 +-
 .../skbio.tree.TreeNode.create_caches.html    |  2 +-
 ...ree.TreeNode.descending_branch_length.html |  2 +-
 .../skbio.tree.TreeNode.distance.html         |  2 +-
 .../generated/skbio.tree.TreeNode.find.html   |  2 +-
 .../skbio.tree.TreeNode.find_all.html         |  2 +-
 .../skbio.tree.TreeNode.find_by_func.html     |  2 +-
 .../skbio.tree.TreeNode.find_by_id.html       |  2 +-
 ...bio.tree.TreeNode.from_linkage_matrix.html |  2 +-
 .../skbio.tree.TreeNode.from_taxdump.html     |  2 +-
 .../skbio.tree.TreeNode.from_taxonomy.html    |  2 +-
 .../skbio.tree.TreeNode.get_max_distance.html |  2 +-
 .../skbio.tree.TreeNode.has_caches.html       |  2 +-
 docs/dev/generated/skbio.tree.TreeNode.html   |  3 +-
 .../skbio.tree.TreeNode.index_tree.html       |  2 +-
 ...skbio.tree.TreeNode.invalidate_caches.html |  2 +-
 .../skbio.tree.TreeNode.is_bifurcating.html   |  2 +-
 ...io.tree.TreeNode.observed_node_counts.html |  2 +-
 .../skbio.tree.TreeNode.root_at.html          |  2 +-
 .../skbio.tree.TreeNode.root_at_midpoint.html |  2 +-
 .../skbio.tree.TreeNode.root_by_outgroup.html |  2 +-
 .../skbio.tree.TreeNode.shuffle.html          | 59 ++++++++++---------
 .../generated/skbio.tree.TreeNode.subset.html |  2 +-
 .../skbio.tree.TreeNode.subsets.html          |  2 +-
 ...skbio.tree.TreeNode.tip_tip_distances.html |  2 +-
 .../skbio.tree.TreeNode.to_array.html         |  2 +-
 .../skbio.tree.TreeNode.to_taxonomy.html      |  2 +-
 .../generated/skbio.tree.TreeNode.unroot.html |  2 +-
 .../skbio.tree.TreeNode.unrooted_copy.html    |  2 +-
 ...skbio.tree.TreeNode.unrooted_deepcopy.html |  2 +-
 .../skbio.tree.TreeNode.unrooted_move.html    |  2 +-
 docs/dev/searchindex.js                       |  2 +-
 docs/dev/tree.html                            |  1 +
 42 files changed, 92 insertions(+), 83 deletions(-)

diff --git a/docs/dev/generated/skbio.tree.TreeNode.accumulate_to_ancestor.html b/docs/dev/generated/skbio.tree.TreeNode.accumulate_to_ancestor.html
index badb86505..14adc2b7b 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.accumulate_to_ancestor.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.accumulate_to_ancestor.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.accumulate_to_ancestor<a class="headerlink" href="#skbio-tree-treenode-accumulate-to-ancestor" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.accumulate_to_ancestor">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">accumulate_to_ancestor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ancestor</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3205"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.accumulate_to_ancestor" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">accumulate_to_ancestor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ancestor</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3212"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.accumulate_to_ancestor" title="Link to this definition">#</a></dt>
 <dd><p>Calculate the distance between self and an ancestor.</p>
 <p>The distance is the sum of branch lengths connecting the current node and the
 given ancestral node.</p>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.ascii_art.html b/docs/dev/generated/skbio.tree.TreeNode.ascii_art.html
index 23a98eac8..68fdf92e4 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.ascii_art.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.ascii_art.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.ascii_art<a class="headerlink" href="#skbio-tree-treenode-ascii-art" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.ascii_art">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">ascii_art</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">show_internal</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">compact</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4452"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.ascii_art" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">ascii_art</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">show_internal</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">compact</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4462"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.ascii_art" title="Link to this definition">#</a></dt>
 <dd><p>Return a string containing an ascii drawing of the tree.</p>
 <p>Note, this method calls a private recursive function and is not safe
 for large trees.</p>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.assign_ids.html b/docs/dev/generated/skbio.tree.TreeNode.assign_ids.html
index 1dfae947e..257c70362 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.assign_ids.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.assign_ids.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.assign_ids<a class="headerlink" href="#skbio-tree-treenode-assign-ids" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.assign_ids">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">assign_ids</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4068"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.assign_ids" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">assign_ids</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4078"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.assign_ids" title="Link to this definition">#</a></dt>
 <dd><p>Assign topologically stable unique IDs to all nodes of the tree.</p>
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.assign_supports.html b/docs/dev/generated/skbio.tree.TreeNode.assign_supports.html
index 8c82ee0d7..2cc6a3950 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.assign_supports.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.assign_supports.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.assign_supports<a class="headerlink" href="#skbio-tree-treenode-assign-supports" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.assign_supports">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">assign_supports</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3068"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.assign_supports" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">assign_supports</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3075"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.assign_supports" title="Link to this definition">#</a></dt>
 <dd><p>Extract support values from internal node labels of a tree.</p>
 <p class="rubric">Notes</p>
 <p>A “support value” measures the confidence or frequency of the incoming
diff --git a/docs/dev/generated/skbio.tree.TreeNode.cache_attr.html b/docs/dev/generated/skbio.tree.TreeNode.cache_attr.html
index a1c18a4c8..684901eb3 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.cache_attr.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.cache_attr.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.cache_attr<a class="headerlink" href="#skbio-tree-treenode-cache-attr" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.cache_attr">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">cache_attr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">func</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_attrname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_type=&lt;class</span> <span class="pre">'list'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">register=True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3917"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.cache_attr" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">cache_attr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">func</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_attrname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_type=&lt;class</span> <span class="pre">'list'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">register=True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3927"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.cache_attr" title="Link to this definition">#</a></dt>
 <dd><p>Cache attributes on nodes of the tree through a postorder traversal.</p>
 <dl class="field-list">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.clear_caches.html b/docs/dev/generated/skbio.tree.TreeNode.clear_caches.html
index 7b14fe2be..7ceb41810 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.clear_caches.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.clear_caches.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.clear_caches<a class="headerlink" href="#skbio-tree-treenode-clear-caches" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.clear_caches">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">clear_caches</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">attr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lookup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3844"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.clear_caches" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">clear_caches</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">attr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lookup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3854"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.clear_caches" title="Link to this definition">#</a></dt>
 <dd><p>Delete node attribute and lookup caches of a tree.</p>
 <div class="versionchanged">
 <p><span class="versionmodified changed">Changed in version 0.6.3: </span>Renamed from <code class="docutils literal notranslate"><span class="pre">invalidate_caches</span></code>. The old name is preserved as an alias.
diff --git a/docs/dev/generated/skbio.tree.TreeNode.compare_rfd.html b/docs/dev/generated/skbio.tree.TreeNode.compare_rfd.html
index 026bbbf05..3f0efa07d 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.compare_rfd.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.compare_rfd.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.compare_rfd<a class="headerlink" href="#skbio-tree-treenode-compare-rfd" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.compare_rfd">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">compare_rfd</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">proportion</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3582"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.compare_rfd" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">compare_rfd</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">proportion</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3589"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.compare_rfd" title="Link to this definition">#</a></dt>
 <dd><p>Calculate the Robinson and Foulds symmetric difference.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.compare_subsets.html b/docs/dev/generated/skbio.tree.TreeNode.compare_subsets.html
index 02b43e46f..369faf9b8 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.compare_subsets.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.compare_subsets.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.compare_subsets<a class="headerlink" href="#skbio-tree-treenode-compare-subsets" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.compare_subsets">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">compare_subsets</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_absent_taxa</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3653"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.compare_subsets" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">compare_subsets</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_absent_taxa</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3660"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.compare_subsets" title="Link to this definition">#</a></dt>
 <dd><p>Return fraction of overlapping subsets where self and other differ.</p>
 <p>Names present in only one of the two trees will count as mismatches,
 if you don’t want this behavior, strip out the non-matching tips first.</p>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.compare_tip_distances.html b/docs/dev/generated/skbio.tree.TreeNode.compare_tip_distances.html
index 6f0ca4213..0419fd168 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.compare_tip_distances.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.compare_tip_distances.html
@@ -59,6 +59,7 @@
                 gtag('js', new Date());
                 gtag('config', 'UA-6636235-9');
             </script>
+    <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'generated/skbio.tree.TreeNode.compare_tip_distances';</script>
     <script>
         DOCUMENTATION_OPTIONS.theme_version = '0.15.4';
@@ -769,24 +770,28 @@
 <h1>skbio.tree.TreeNode.compare_tip_distances<a class="headerlink" href="#skbio-tree-treenode-compare-tip-distances" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.compare_tip_distances">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">compare_tip_distances</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sample=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dist_f=&lt;function</span> <span class="pre">distance_from_r&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shuffle_f=&lt;bound</span> <span class="pre">method</span> <span class="pre">RandomState.shuffle</span> <span class="pre">of</span> <span class="pre">RandomState(MT19937)&gt;</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3703"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.compare_tip_distances" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">compare_tip_distances</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sample</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">dist_f</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">shuffle_f</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 external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3710"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.compare_tip_distances" title="Link to this definition">#</a></dt>
 <dd><p>Compare self to other using tip-to-tip distance matrices.</p>
-<p>Value returned is <cite>dist_f(m1, m2)</cite> for the two matrices. Default is to use the
-Pearson correlation coefficient, with +1 giving a distance of 0 and -1 giving a
-distance of +1 (the maximum possible value). Depending on the application, you
-might instead want to use distance_from_r_squared, which counts correlations of
-both +1 and -1 as identical (0 distance).</p>
-<dl class="field-list simple">
+<dl class="field-list">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><dl class="simple">
-<dt><strong>other</strong><span class="classifier">TreeNode</span></dt><dd><p>The tree to compare</p>
+<dd class="field-odd"><dl>
+<dt><strong>other</strong><span class="classifier">TreeNode</span></dt><dd><p>The tree to compare.</p>
 </dd>
 <dt><strong>sample</strong><span class="classifier">int, optional</span></dt><dd><p>Randomly subsample this number of tips in common between the trees to
 compare. This is useful when comparing very large trees.</p>
 </dd>
-<dt><strong>dist_f</strong><span class="classifier">callable, optional</span></dt><dd><p>The distance function used to compare two the tip-tip distance matrices.</p>
+<dt><strong>dist_f</strong><span class="classifier">callable, optional</span></dt><dd><p>The distance function used to compare two the tip-tip distance matrices.
+Default is <span class="math notranslate nohighlight">\((1-r)/2\)</span>, where <span class="math notranslate nohighlight">\(r\)</span> is the Pearson correlation
+coefficient between the two matrices.</p>
 </dd>
-<dt><strong>shuffle_f</strong><span class="classifier">callable, optional</span></dt><dd><p>The shuffling function used if <code class="docutils literal notranslate"><span class="pre">sample</span></code> is not None.</p>
+<dt><strong>shuffle_f</strong><span class="classifier">int, np.random.Generator or callable, optional</span></dt><dd><p>The shuffling function used if <code class="docutils literal notranslate"><span class="pre">sample</span></code> is specified. Default is the
+<a class="reference external" href="https://numpy.org/doc/stable/reference/random/generated/numpy.random.Generator.shuffle.html#numpy.random.Generator.shuffle" title="(in NumPy v2.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">shuffle</span></code></a> method of a NumPy random
+generator. If an integer is provided, a random generator will be
+constructed using this number as the seed.</p>
+<div class="versionchanged">
+<p><span class="versionmodified changed">Changed in version 0.6.3: </span>Switched to NumPy’s new random generator. Can accept a random seed or
+random generator instance.</p>
+</div>
 </dd>
 </dl>
 </dd>
@@ -808,8 +813,7 @@ <h1>skbio.tree.TreeNode.compare_tip_distances<a class="headerlink" href="#skbio-
 <dl class="simple">
 <dt><a class="reference internal" href="skbio.tree.TreeNode.compare_subsets.html#skbio.tree.TreeNode.compare_subsets" title="skbio.tree.TreeNode.compare_subsets"><code class="xref py py-obj docutils literal notranslate"><span class="pre">compare_subsets</span></code></a></dt><dd></dd>
 <dt><a class="reference internal" href="skbio.tree.TreeNode.compare_rfd.html#skbio.tree.TreeNode.compare_rfd" title="skbio.tree.TreeNode.compare_rfd"><code class="xref py py-obj docutils literal notranslate"><span class="pre">compare_rfd</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://numpy.org/doc/stable/reference/random/generated/numpy.random.shuffle.html#numpy.random.shuffle" title="(in NumPy v2.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numpy.random.shuffle</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://numpy.org/doc/stable/reference/random/generated/numpy.random.Generator.shuffle.html#numpy.random.Generator.shuffle" title="(in NumPy v2.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numpy.random.Generator.shuffle</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.correlation.html#scipy.spatial.distance.correlation" title="(in SciPy v1.14.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.spatial.distance.correlation</span></code></a></dt><dd></dd>
 </dl>
 </div>
 <p class="rubric">Notes</p>
@@ -818,12 +822,10 @@ <h1>skbio.tree.TreeNode.compare_tip_distances<a class="headerlink" href="#skbio-
 matching names is undefined in the tree where they don’t match, and because
 one needs to reorder the names in the two trees to match up the distance
 matrices.</p>
-<p>The default shuffling function is stochastic. To ensure the reproducibility of
-the result, you should use a generator-based function, such as <code class="docutils literal notranslate"><span class="pre">rng.shuffle</span></code>
-where <code class="docutils literal notranslate"><span class="pre">rng</span></code> is a pre-constructed random generator.</p>
 <p class="rubric">Examples</p>
+<p>Calculate the distance between two trees. Note that only three taxa are shared
+between the trees.</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">skbio</span> <span class="kn">import</span> <span class="n">TreeNode</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="c1"># note, only three common taxa between the trees</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">tree1</span> <span class="o">=</span> <span class="n">TreeNode</span><span class="o">.</span><span class="n">read</span><span class="p">([</span><span class="s2">&quot;((a:1,b:1):2,(c:0.5,X:0.7):3);&quot;</span><span class="p">])</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">tree2</span> <span class="o">=</span> <span class="n">TreeNode</span><span class="o">.</span><span class="n">read</span><span class="p">([</span><span class="s2">&quot;(((a:1,b:1,Y:1):2,c:3):1,Z:4);&quot;</span><span class="p">])</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">dist</span> <span class="o">=</span> <span class="n">tree1</span><span class="o">.</span><span class="n">compare_tip_distances</span><span class="p">(</span><span class="n">tree2</span><span class="p">)</span>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.count.html b/docs/dev/generated/skbio.tree.TreeNode.count.html
index cd5837883..1d078260f 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.count.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.count.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.count<a class="headerlink" href="#skbio-tree-treenode-count" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.count">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tips</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2932"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.count" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tips</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2939"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.count" title="Link to this definition">#</a></dt>
 <dd><p>Get the count of nodes in the tree.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.create_caches.html b/docs/dev/generated/skbio.tree.TreeNode.create_caches.html
index f97a82cfa..b9bdb5364 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.create_caches.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.create_caches.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.create_caches<a class="headerlink" href="#skbio-tree-treenode-create-caches" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.create_caches">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">create_caches</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4133"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.create_caches" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">create_caches</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4143"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.create_caches" title="Link to this definition">#</a></dt>
 <dd><p>Construct an internal lookup table to facilitate searching by name.</p>
 <div class="deprecated">
 <p><span class="versionmodified deprecated">Deprecated since version 0.6.3: </span>This method will become a private member in version 0.7.0. It is meant to
diff --git a/docs/dev/generated/skbio.tree.TreeNode.descending_branch_length.html b/docs/dev/generated/skbio.tree.TreeNode.descending_branch_length.html
index cd0779175..8a489b6f3 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.descending_branch_length.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.descending_branch_length.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.descending_branch_length<a class="headerlink" href="#skbio-tree-treenode-descending-branch-length" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.descending_branch_length">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">descending_branch_length</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tip_subset</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 external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3258"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.descending_branch_length" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">descending_branch_length</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tip_subset</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 external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3265"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.descending_branch_length" title="Link to this definition">#</a></dt>
 <dd><p>Find total descending branch length from self to a set of tips.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.distance.html b/docs/dev/generated/skbio.tree.TreeNode.distance.html
index 0766f1a00..d689583b4 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.distance.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.distance.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.distance<a class="headerlink" href="#skbio-tree-treenode-distance" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.distance">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">distance</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3322"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.distance" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">distance</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3329"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.distance" title="Link to this definition">#</a></dt>
 <dd><p>Calculate the distance between self and another node.</p>
 <p>This method can be used to compute the distances between two tips,
 however, it is not optimized for computing pairwise tip distances.</p>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.find.html b/docs/dev/generated/skbio.tree.TreeNode.find.html
index 307c87a58..915781b4c 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.find.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.find.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.find<a class="headerlink" href="#skbio-tree-treenode-find" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.find">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">find</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4186"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.find" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">find</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4196"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.find" title="Link to this definition">#</a></dt>
 <dd><p>Find a node by name.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.find_all.html b/docs/dev/generated/skbio.tree.TreeNode.find_all.html
index 121d63933..7c2b1243a 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.find_all.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.find_all.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.find_all<a class="headerlink" href="#skbio-tree-treenode-find-all" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.find_all">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">find_all</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4253"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.find_all" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">find_all</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4263"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.find_all" title="Link to this definition">#</a></dt>
 <dd><p>Find all nodes that match a given name.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.find_by_func.html b/docs/dev/generated/skbio.tree.TreeNode.find_by_func.html
index e06ec0547..23cb8dc6a 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.find_by_func.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.find_by_func.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.find_by_func<a class="headerlink" href="#skbio-tree-treenode-find-by-func" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.find_by_func">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">find_by_func</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">func</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4373"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.find_by_func" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">find_by_func</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">func</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4383"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.find_by_func" title="Link to this definition">#</a></dt>
 <dd><p>Find all nodes in a tree that meet certain criteria.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.find_by_id.html b/docs/dev/generated/skbio.tree.TreeNode.find_by_id.html
index 29bc3554c..6163858c3 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.find_by_id.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.find_by_id.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.find_by_id<a class="headerlink" href="#skbio-tree-treenode-find-by-id" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.find_by_id">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">find_by_id</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">node_id</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4329"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.find_by_id" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">find_by_id</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">node_id</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4339"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.find_by_id" title="Link to this definition">#</a></dt>
 <dd><p>Find a node by ID.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.from_linkage_matrix.html b/docs/dev/generated/skbio.tree.TreeNode.from_linkage_matrix.html
index bce180ffc..40db37440 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.from_linkage_matrix.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.from_linkage_matrix.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.from_linkage_matrix<a class="headerlink" href="#skbio-tree-treenode-from-linkage-matrix" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.from_linkage_matrix">
-<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">from_linkage_matrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">linkage_matrix</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_list</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4510"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.from_linkage_matrix" title="Link to this definition">#</a></dt>
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">from_linkage_matrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">linkage_matrix</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_list</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4520"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.from_linkage_matrix" title="Link to this definition">#</a></dt>
 <dd><p>Return tree from SciPy linkage matrix.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.from_taxdump.html b/docs/dev/generated/skbio.tree.TreeNode.from_taxdump.html
index ca84dd808..138d4a7a5 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.from_taxdump.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.from_taxdump.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.from_taxdump<a class="headerlink" href="#skbio-tree-treenode-from-taxdump" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.from_taxdump">
-<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">from_taxdump</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nodes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">names</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 external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4729"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.from_taxdump" title="Link to this definition">#</a></dt>
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">from_taxdump</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nodes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">names</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 external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4739"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.from_taxdump" title="Link to this definition">#</a></dt>
 <dd><p>Construct a tree from the NCBI taxonomy database.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.from_taxonomy.html b/docs/dev/generated/skbio.tree.TreeNode.from_taxonomy.html
index 7f908019c..fff76ef9a 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.from_taxonomy.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.from_taxonomy.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.from_taxonomy<a class="headerlink" href="#skbio-tree-treenode-from-taxonomy" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.from_taxonomy">
-<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">from_taxonomy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lineage_map</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4559"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.from_taxonomy" title="Link to this definition">#</a></dt>
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">from_taxonomy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lineage_map</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4569"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.from_taxonomy" title="Link to this definition">#</a></dt>
 <dd><p>Construct a tree from a taxonomy.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.get_max_distance.html b/docs/dev/generated/skbio.tree.TreeNode.get_max_distance.html
index bd7193cfa..5899704f8 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.get_max_distance.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.get_max_distance.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.get_max_distance<a class="headerlink" href="#skbio-tree-treenode-get-max-distance" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.get_max_distance">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">get_max_distance</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3415"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.get_max_distance" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">get_max_distance</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3422"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.get_max_distance" title="Link to this definition">#</a></dt>
 <dd><p>Return the max tip tip distance between any pair of tips.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.has_caches.html b/docs/dev/generated/skbio.tree.TreeNode.has_caches.html
index 3ba633a43..6655efbc1 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.has_caches.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.has_caches.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.has_caches<a class="headerlink" href="#skbio-tree-treenode-has-caches" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.has_caches">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">has_caches</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3793"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.has_caches" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">has_caches</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3803"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.has_caches" title="Link to this definition">#</a></dt>
 <dd><p>Check if the current tree has caches.</p>
 <div class="versionadded">
 <p><span class="versionmodified added">Added in version 0.6.3.</span></p>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.html b/docs/dev/generated/skbio.tree.TreeNode.html
index d3a9efa35..cea753743 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.html
@@ -59,6 +59,7 @@
                 gtag('js', new Date());
                 gtag('config', 'UA-6636235-9');
             </script>
+    <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'generated/skbio.tree.TreeNode';</script>
     <script>
         DOCUMENTATION_OPTIONS.theme_version = '0.15.4';
@@ -934,7 +935,7 @@ <h1>skbio.tree.TreeNode<a class="headerlink" href="#skbio-tree-treenode" title="
 <td><p>Convert the tree into a bifurcating tree.</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="skbio.tree.TreeNode.shuffle.html#skbio.tree.TreeNode.shuffle" title="skbio.tree.TreeNode.shuffle"><code class="xref py py-obj docutils literal notranslate"><span class="pre">shuffle</span></code></a>([k, names, shuffle_f, n])</p></td>
-<td><p>Yield trees with shuffled tip names.</p></td>
+<td><p>Shuffled tip names of the tree.</p></td>
 </tr>
 </tbody>
 </table>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.index_tree.html b/docs/dev/generated/skbio.tree.TreeNode.index_tree.html
index 5bc31dd07..63c63a3cc 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.index_tree.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.index_tree.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.index_tree<a class="headerlink" href="#skbio-tree-treenode-index-tree" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.index_tree">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">index_tree</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4092"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.index_tree" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">index_tree</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4102"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.index_tree" title="Link to this definition">#</a></dt>
 <dd><p>Index a tree for rapid lookups within a tree array.</p>
 <p>Indexes nodes in-place as <code class="docutils literal notranslate"><span class="pre">n._leaf_index</span></code>.</p>
 <dl class="field-list simple">
diff --git a/docs/dev/generated/skbio.tree.TreeNode.invalidate_caches.html b/docs/dev/generated/skbio.tree.TreeNode.invalidate_caches.html
index 573e4bb74..69ef56551 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.invalidate_caches.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.invalidate_caches.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.invalidate_caches<a class="headerlink" href="#skbio-tree-treenode-invalidate-caches" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.invalidate_caches">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">invalidate_caches</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">attr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lookup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3844"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.invalidate_caches" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">invalidate_caches</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">attr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lookup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3854"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.invalidate_caches" title="Link to this definition">#</a></dt>
 <dd><p>Delete node attribute and lookup caches of a tree.</p>
 <div class="versionchanged">
 <p><span class="versionmodified changed">Changed in version 0.6.3: </span>Renamed from <code class="docutils literal notranslate"><span class="pre">invalidate_caches</span></code>. The old name is preserved as an alias.
diff --git a/docs/dev/generated/skbio.tree.TreeNode.is_bifurcating.html b/docs/dev/generated/skbio.tree.TreeNode.is_bifurcating.html
index 45f228e2c..6d9143feb 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.is_bifurcating.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.is_bifurcating.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.is_bifurcating<a class="headerlink" href="#skbio-tree-treenode-is-bifurcating" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.is_bifurcating">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">is_bifurcating</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3122"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.is_bifurcating" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">is_bifurcating</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3129"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.is_bifurcating" title="Link to this definition">#</a></dt>
 <dd><p>Check if the tree is bifurcating.</p>
 <div class="versionadded">
 <p><span class="versionmodified added">Added in version 0.6.3.</span></p>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.observed_node_counts.html b/docs/dev/generated/skbio.tree.TreeNode.observed_node_counts.html
index c9413c516..5e8620a9c 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.observed_node_counts.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.observed_node_counts.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.observed_node_counts<a class="headerlink" href="#skbio-tree-treenode-observed-node-counts" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.observed_node_counts">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">observed_node_counts</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tip_counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3165"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.observed_node_counts" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">observed_node_counts</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tip_counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3172"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.observed_node_counts" title="Link to this definition">#</a></dt>
 <dd><p>Return counts of node observations from counts of tip observations.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.root_at.html b/docs/dev/generated/skbio.tree.TreeNode.root_at.html
index 2c47f7ab9..7a4870648 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.root_at.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.root_at.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.root_at<a class="headerlink" href="#skbio-tree-treenode-root-at" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.root_at">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">root_at</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">node</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">above</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">branch_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">['name']</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">root_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'root'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inplace</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2365"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.root_at" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">root_at</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">node</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">above</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">branch_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">['name']</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">root_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'root'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inplace</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2372"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.root_at" title="Link to this definition">#</a></dt>
 <dd><p>Reroot the tree at the provided node.</p>
 <p>This is useful for positioning a tree with an orientation that reflects
 knowledge of the true root location.</p>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.root_at_midpoint.html b/docs/dev/generated/skbio.tree.TreeNode.root_at_midpoint.html
index 3899ca431..3ae041b76 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.root_at_midpoint.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.root_at_midpoint.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.root_at_midpoint<a class="headerlink" href="#skbio-tree-treenode-root-at-midpoint" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.root_at_midpoint">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">root_at_midpoint</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">branch_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">['name']</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">root_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'root'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inplace</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2593"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.root_at_midpoint" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">root_at_midpoint</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">branch_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">['name']</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">root_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'root'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inplace</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2600"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.root_at_midpoint" title="Link to this definition">#</a></dt>
 <dd><p>Reroot the tree at the midpoint of the two tips farthest apart.</p>
 <dl class="field-list">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.root_by_outgroup.html b/docs/dev/generated/skbio.tree.TreeNode.root_by_outgroup.html
index 9c34b1758..96b84edd1 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.root_by_outgroup.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.root_by_outgroup.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.root_by_outgroup<a class="headerlink" href="#skbio-tree-treenode-root-by-outgroup" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.root_by_outgroup">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">root_by_outgroup</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">outgroup</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">above</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">branch_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">root_name</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">inplace</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2765"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.root_by_outgroup" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">root_by_outgroup</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">outgroup</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">above</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">branch_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">root_name</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">inplace</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2772"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.root_by_outgroup" title="Link to this definition">#</a></dt>
 <dd><p>Reroot the tree with a given set of taxa as outgroup.</p>
 <div class="versionadded">
 <p><span class="versionmodified added">Added in version 0.6.2.</span></p>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.shuffle.html b/docs/dev/generated/skbio.tree.TreeNode.shuffle.html
index 6310c80fc..3130fc2ac 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.shuffle.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.shuffle.html
@@ -6,7 +6,7 @@
 
   <head>
     <meta charset="utf-8" />
-    <meta name="description" content="Yield trees with shuffled tip names." />
+    <meta name="description" content="Shuffled tip names of the tree." />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
     <title>skbio.tree.TreeNode.shuffle &#8212; scikit-bio 0.6.3-dev documentation</title>
@@ -769,20 +769,31 @@
 <h1>skbio.tree.TreeNode.shuffle<a class="headerlink" href="#skbio-tree-treenode-shuffle" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.shuffle">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">shuffle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">k=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">names=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shuffle_f=&lt;bound</span> <span class="pre">method</span> <span class="pre">RandomState.shuffle</span> <span class="pre">of</span> <span class="pre">RandomState(MT19937)&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n=1</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L1859"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.shuffle" title="Link to this definition">#</a></dt>
-<dd><p>Yield trees with shuffled tip names.</p>
-<dl class="field-list simple">
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">shuffle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">k</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">names</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">shuffle_f</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">n</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L1859"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.shuffle" title="Link to this definition">#</a></dt>
+<dd><p>Shuffled tip names of the tree.</p>
+<dl class="field-list">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><dl class="simple">
-<dt><strong>k</strong><span class="classifier">int, optional</span></dt><dd><p>The number of tips to shuffle. If not None, this number of tips are
-randomly selected, and only those names will be shuffled.</p>
+<dd class="field-odd"><dl>
+<dt><strong>k</strong><span class="classifier">int, optional</span></dt><dd><p>The number of tips to shuffle. If provided, this number of tips will be
+randomly selected by <code class="docutils literal notranslate"><span class="pre">shuffle_f</span></code>, and only those names will be shuffled.
+Conflicts with <code class="docutils literal notranslate"><span class="pre">names</span></code>.</p>
 </dd>
-<dt><strong>names</strong><span class="classifier">list, optional</span></dt><dd><p>The specific tip names to shuffle.</p>
+<dt><strong>names</strong><span class="classifier">list, optional</span></dt><dd><p>The specific tip names to shuffle. Conflicts with <code class="docutils literal notranslate"><span class="pre">k</span></code>.</p>
 </dd>
-<dt><strong>shuffle_f</strong><span class="classifier">callable, optional</span></dt><dd><p>Shuffling function, which must accept a list and modify inplace.</p>
+<dt><strong>shuffle_f</strong><span class="classifier">int, np.random.Generator or callable, optional</span></dt><dd><p>Shuffling function, which must accept a list and modify in place. Default
+is the <a class="reference external" href="https://numpy.org/doc/stable/reference/random/generated/numpy.random.Generator.shuffle.html#numpy.random.Generator.shuffle" title="(in NumPy v2.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">shuffle</span></code></a> method of a NumPy
+random generator. If an integer is provided, a random generator will be
+constructed using this number as the seed.</p>
+<div class="versionchanged">
+<p><span class="versionmodified changed">Changed in version 0.6.3: </span>Switched to NumPy’s new random generator. Can accept a random seed or
+random generator instance.</p>
+</div>
 </dd>
-<dt><strong>n</strong><span class="classifier">int, optional</span></dt><dd><p>The number of iterations to perform. Value must be &gt; 0 and <code class="docutils literal notranslate"><span class="pre">np.inf</span></code> can
-be specified for an infinite number of iterations.</p>
+<dt><strong>n</strong><span class="classifier">int, optional</span></dt><dd><p>The number of iterations to perform. Must be a positive integer. Default
+is 1. If None or <code class="docutils literal notranslate"><span class="pre">np.inf</span></code>, iterations will be infinite.</p>
+<div class="versionchanged">
+<p><span class="versionmodified changed">Changed in version 0.6.3: </span>Can accept None.</p>
+</div>
 </dd>
 </dl>
 </dd>
@@ -806,7 +817,6 @@ <h1>skbio.tree.TreeNode.shuffle<a class="headerlink" href="#skbio-tree-treenode-
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
 <dl class="simple">
-<dt><a class="reference external" href="https://numpy.org/doc/stable/reference/random/generated/numpy.random.shuffle.html#numpy.random.shuffle" title="(in NumPy v2.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numpy.random.shuffle</span></code></a></dt><dd></dd>
 <dt><a class="reference external" href="https://numpy.org/doc/stable/reference/random/generated/numpy.random.Generator.shuffle.html#numpy.random.Generator.shuffle" title="(in NumPy v2.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numpy.random.Generator.shuffle</span></code></a></dt><dd></dd>
 </dl>
 </div>
@@ -814,28 +824,23 @@ <h1>skbio.tree.TreeNode.shuffle<a class="headerlink" href="#skbio-tree-treenode-
 <p>This method does not create copies of the tree. Instead, tip names are shuffled
 in place in the original tree and the tree is yielded prior to the next round
 of shuffling. Tree caches will be cleared prior to shuffling.</p>
-<p><code class="docutils literal notranslate"><span class="pre">k</span></code> and <code class="docutils literal notranslate"><span class="pre">names</span></code> cannot be specified at the same time, or an error will be
-raised. If neither <code class="docutils literal notranslate"><span class="pre">k</span></code> nor <code class="docutils literal notranslate"><span class="pre">names</span></code> are provided, all tips are shuffled.</p>
-<p>The default shuffling function is stochastic. To ensure the reproducibility of
-the result, you should use a generator-based function, such as <code class="docutils literal notranslate"><span class="pre">rng.shuffle</span></code>
-where <code class="docutils literal notranslate"><span class="pre">rng</span></code> is a pre-constructed random generator.</p>
+<p><code class="docutils literal notranslate"><span class="pre">k</span></code> and <code class="docutils literal notranslate"><span class="pre">names</span></code> cannot be specified at the same time. If neither <code class="docutils literal notranslate"><span class="pre">k</span></code> nor
+<code class="docutils literal notranslate"><span class="pre">names</span></code> are provided, all tips will be shuffled.</p>
 <p class="rubric">Examples</p>
-<p>Alternate the names on two of the tips, ‘a’, and ‘b’, and do this 5 times:</p>
+<p>Shuffle the names of a 4-tip tree for 5 times:</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">skbio</span> <span class="kn">import</span> <span class="n">TreeNode</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">tree</span> <span class="o">=</span> <span class="n">TreeNode</span><span class="o">.</span><span class="n">read</span><span class="p">([</span><span class="s2">&quot;((a,b),(c,d));&quot;</span><span class="p">])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">rev</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">items</span><span class="p">:</span> <span class="n">items</span><span class="o">.</span><span class="n">reverse</span><span class="p">()</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">shuffler</span> <span class="o">=</span> <span class="n">tree</span><span class="o">.</span><span class="n">shuffle</span><span class="p">(</span><span class="n">names</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">],</span> <span class="n">shuffle_f</span><span class="o">=</span><span class="n">rev</span><span class="p">,</span> <span class="n">n</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="k">for</span> <span class="n">shuffled_tree</span> <span class="ow">in</span> <span class="n">shuffler</span><span class="p">:</span>
-<span class="gp">... </span>    <span class="nb">print</span><span class="p">(</span><span class="n">shuffled_tree</span><span class="p">)</span>
-<span class="go">((b,a),(c,d));</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="k">for</span> <span class="n">shuffled</span> <span class="ow">in</span> <span class="n">tree</span><span class="o">.</span><span class="n">shuffle</span><span class="p">(</span><span class="n">shuffle_f</span><span class="o">=</span><span class="mi">42</span><span class="p">,</span> <span class="n">n</span><span class="o">=</span><span class="mi">5</span><span class="p">):</span>
+<span class="gp">... </span>    <span class="nb">print</span><span class="p">(</span><span class="n">shuffled</span><span class="p">)</span>
+<span class="go">((d,c),(b,a));</span>
 
-<span class="go">((a,b),(c,d));</span>
+<span class="go">((a,b),(d,c));</span>
 
-<span class="go">((b,a),(c,d));</span>
+<span class="go">((a,c),(d,b));</span>
 
-<span class="go">((a,b),(c,d));</span>
+<span class="go">((d,b),(a,c));</span>
 
-<span class="go">((b,a),(c,d));</span>
+<span class="go">((a,c),(d,b));</span>
 </pre></div>
 </div>
 </dd></dl>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.subset.html b/docs/dev/generated/skbio.tree.TreeNode.subset.html
index 3f8fc1d3f..bad854573 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.subset.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.subset.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.subset<a class="headerlink" href="#skbio-tree-treenode-subset" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.subset">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">subset</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2960"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.subset" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">subset</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2967"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.subset" title="Link to this definition">#</a></dt>
 <dd><p>Return set of tip names that descend from specified node.</p>
 <p>Get the set of <cite>name</cite> on tips that descend from this node.</p>
 <dl class="field-list simple">
diff --git a/docs/dev/generated/skbio.tree.TreeNode.subsets.html b/docs/dev/generated/skbio.tree.TreeNode.subsets.html
index 0a5783f89..40efda429 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.subsets.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.subsets.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.subsets<a class="headerlink" href="#skbio-tree-treenode-subsets" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.subsets">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">subsets</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2985"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.subsets" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">subsets</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2992"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.subsets" title="Link to this definition">#</a></dt>
 <dd><p>Return all sets of tip names that come from self and its descendants.</p>
 <p>Compute all subsets of tip names over <cite>self</cite>, or, represent a tree as a
 set of nested sets.</p>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.tip_tip_distances.html b/docs/dev/generated/skbio.tree.TreeNode.tip_tip_distances.html
index 3242b8e22..8352b4ba3 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.tip_tip_distances.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.tip_tip_distances.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.tip_tip_distances<a class="headerlink" href="#skbio-tree-treenode-tip-tip-distances" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.tip_tip_distances">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">tip_tip_distances</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">endpoints</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 external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3472"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.tip_tip_distances" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">tip_tip_distances</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">endpoints</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 external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3479"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.tip_tip_distances" title="Link to this definition">#</a></dt>
 <dd><p>Return distance matrix between pairs of tips, and a tip order.</p>
 <p>By default, all pairwise distances are calculated in the tree. If
 <cite>endpoints</cite> are specified, then only the distances between those tips
diff --git a/docs/dev/generated/skbio.tree.TreeNode.to_array.html b/docs/dev/generated/skbio.tree.TreeNode.to_array.html
index 16e5e8b83..b7ef4942e 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.to_array.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.to_array.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.to_array<a class="headerlink" href="#skbio-tree-treenode-to-array" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.to_array">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">attrs</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">nan_length_value</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 external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4843"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.to_array" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">attrs</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">nan_length_value</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 external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4853"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.to_array" title="Link to this definition">#</a></dt>
 <dd><p>Return an array representation of self.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.to_taxonomy.html b/docs/dev/generated/skbio.tree.TreeNode.to_taxonomy.html
index 0672f7ebc..39413154a 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.to_taxonomy.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.to_taxonomy.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.to_taxonomy<a class="headerlink" href="#skbio-tree-treenode-to-taxonomy" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.to_taxonomy">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">to_taxonomy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">allow_empty</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filter_f</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 external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4643"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.to_taxonomy" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">to_taxonomy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">allow_empty</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filter_f</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 external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4653"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.to_taxonomy" title="Link to this definition">#</a></dt>
 <dd><p>Return a taxonomy representation of self.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.unroot.html b/docs/dev/generated/skbio.tree.TreeNode.unroot.html
index e7fa74386..6b1255cba 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.unroot.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.unroot.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.unroot<a class="headerlink" href="#skbio-tree-treenode-unroot" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.unroot">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">unroot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">side</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">uncache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L1967"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.unroot" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">unroot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">side</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">uncache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L1974"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.unroot" title="Link to this definition">#</a></dt>
 <dd><p>Convert a rooted tree into unrooted.</p>
 <div class="versionadded">
 <p><span class="versionmodified added">Added in version 0.6.2.</span></p>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.unrooted_copy.html b/docs/dev/generated/skbio.tree.TreeNode.unrooted_copy.html
index b0ea7138f..0bca77fa0 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.unrooted_copy.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.unrooted_copy.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.unrooted_copy<a class="headerlink" href="#skbio-tree-treenode-unrooted-copy" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.unrooted_copy">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">unrooted_copy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</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">branch_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{'length',</span> <span class="pre">'name',</span> <span class="pre">'support'}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">root_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'root'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">deep</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_attrs</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 external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2082"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.unrooted_copy" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">unrooted_copy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</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">branch_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{'length',</span> <span class="pre">'name',</span> <span class="pre">'support'}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">root_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'root'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">deep</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_attrs</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 external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2089"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.unrooted_copy" title="Link to this definition">#</a></dt>
 <dd><p>Walk the tree unrooted-style and return a copy.</p>
 <dl class="field-list">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/dev/generated/skbio.tree.TreeNode.unrooted_deepcopy.html b/docs/dev/generated/skbio.tree.TreeNode.unrooted_deepcopy.html
index 4f38a3a34..ef1d70f28 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.unrooted_deepcopy.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.unrooted_deepcopy.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.unrooted_deepcopy<a class="headerlink" href="#skbio-tree-treenode-unrooted-deepcopy" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.unrooted_deepcopy">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">unrooted_deepcopy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</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 external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2243"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.unrooted_deepcopy" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">unrooted_deepcopy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</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 external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2250"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.unrooted_deepcopy" title="Link to this definition">#</a></dt>
 <dd><p>Walk the tree unrooted-style and returns a new deepcopy.</p>
 <div class="deprecated">
 <p><span class="versionmodified deprecated">Deprecated since version 0.6.2: </span>This function is deprecated as it generates a redundant copy of the tree.
diff --git a/docs/dev/generated/skbio.tree.TreeNode.unrooted_move.html b/docs/dev/generated/skbio.tree.TreeNode.unrooted_move.html
index 82a77cab4..c01404c6f 100644
--- a/docs/dev/generated/skbio.tree.TreeNode.unrooted_move.html
+++ b/docs/dev/generated/skbio.tree.TreeNode.unrooted_move.html
@@ -769,7 +769,7 @@
 <h1>skbio.tree.TreeNode.unrooted_move<a class="headerlink" href="#skbio-tree-treenode-unrooted-move" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.unrooted_move">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">unrooted_move</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</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">branch_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{'length',</span> <span class="pre">'support'}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uncache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2287"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.unrooted_move" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">unrooted_move</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</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">branch_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{'length',</span> <span class="pre">'support'}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uncache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2294"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.unrooted_move" title="Link to this definition">#</a></dt>
 <dd><p>Walk the tree unrooted-style and rearrange it.</p>
 <div class="versionadded">
 <p><span class="versionmodified added">Added in version 0.6.2.</span></p>
diff --git a/docs/dev/searchindex.js b/docs/dev/searchindex.js
index 4d7209b95..def160b72 100644
--- a/docs/dev/searchindex.js
+++ b/docs/dev/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"Abstract classes": [[498, "abstract-classes"], [499, "abstract-classes"]], "Adding Node Information": [[119, "adding-node-information"]], "Advanced Label and Length Rules": [[119, "advanced-label-and-length-rules"]], "Alignment Section": [[111, "alignment-section"], [121, "alignment-section"]], "Alignment algorithms": [[0, "alignment-algorithms"]], "Alignment data structure": [[0, "alignment-data-structure"]], "Alignment structure": [[0, "alignment-structure"]], "Alpha diversity": [[1, "alpha-diversity"]], "Alpha diversity measures (skbio.diversity.alpha)": [[43, null]], "Application of Rules": [[119, "application-of-rules"]], "BIOM table": [[501, "biom-table"]], "BIOM-Format (skbio.io.format.biom)": [[108, null]], "BLAST Column Types": [[109, "blast-column-types"], [110, "blast-column-types"]], "BLAST+6 format (skbio.io.format.blast6)": [[109, null]], "BLAST+7 format (skbio.io.format.blast7)": [[110, null]], "Basic Symbols": [[119, "basic-symbols"]], "Beta diversity": [[1, "beta-diversity"]], "Beta diversity measures (skbio.diversity.beta)": [[84, null]], "Biological Embeddings (skbio.embedding)": [[2, null]], "Biological Sequences (skbio.sequence)": [[499, null]], "Canonical analysis": [[327, "canonical-analysis"]], "Categorical Variable Stats": [[282, "categorical-variable-stats"]], "Caveats": [[119, "caveats"]], "Classes": [[126, "classes"], [282, "classes"], [313, "classes"], [504, "classes"]], "Clustal format (skbio.io.format.clustal)": [[111, null]], "Column Types": [[123, "column-types"]], "Comments and Empty Rows": [[123, "comments-and-empty-rows"]], "Community Diversity (skbio.diversity)": [[1, null]], "Composition Statistics (skbio.stats.composition)": [[261, null]], "Composition statistics": [[500, "composition-statistics"]], "Continuous Variable Stats": [[282, "continuous-variable-stats"]], "Cophylogenetic methods": [[311, "cophylogenetic-methods"]], "Correspondence analysis": [[327, "correspondence-analysis"]], "Count vectors": [[1, "count-vectors"]], "Coverage metrics": [[43, "coverage-metrics"]], "Creating a new format for scikit-bio": [[126, "creating-a-new-format-for-scikit-bio"]], "Data Table (skbio.table)": [[501, null]], "Data structures": [[282, "data-structures"]], "Data subsampling": [[500, "data-subsampling"]], "Decorators": [[504, "decorators"]], "Deprecated functionality": [[0, "deprecated-functionality"]], "Details": [[503, "details"]], "Develop custom formats": [[497, "develop-custom-formats"]], "Developer warnings": [[503, "developer-warnings"]], "Distance Matrix Comparisons": [[282, "distance-matrix-comparisons"]], "Distance calculation": [[499, "distance-calculation"]], "Distance matrix statistics": [[500, "distance-matrix-statistics"]], "Distance matrix-based statistics (skbio.stats.distance)": [[282, null]], "Distance-based statistics": [[282, "distance-based-statistics"]], "Diversity metrics": [[43, "diversity-metrics"]], "Dominance metrics": [[43, "dominance-metrics"]], "EMBL 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121], "aaacccttgccg": 114, "aaacccttgccggtacgcttaaaccattgccggtacgcttaa": 114, "aaacccttgccgttacgcttaaaccgaggccgggacactcat": 114, "aaaccgaggc": [114, 121], "aaagataggc": 113, "aaatatggat": 113, "aaatcctatg": 113, "aac": 122, "aacaaatgca": 113, "aacaacagga": 113, "aacaccaaacttctccacc": 115, "aacaccaaacttctccaccacgtgagctacaaaag": 115, "aaccttatca": 113, "aacga": 233, "aacgaaggcg": 113, "aacgac": 233, "aactttgtag": 113, "aagaactttc": 113, "aagaggttac": 113, "aagcctggtg": 113, "aagccttggc": 114, "aagccttggcagtgcagggtgagccgtgg": 114, "aagccttggcagtgcagggtgagccgtggccgggcacggtat": 114, "aagctngggc": [114, 121], "aagctngggcatttcagggtgagcccgggcaatacagggtat": 114, "aagga": 233, "aaggaatcaa": 113, "aaggaatttg": 113, "aagtaa": 215, "aagtatttgg": 113, "aagtcttaga": 113, "aagtcttttt": 113, "aagttgttag": 113, "aagucuuuuu": 113, "aata": 122, "aataaac": 122, "aataagtgca": 113, "aatacagggt": [114, 121], "aatataccggttataa": 237, "aatatggatt": 113, "aatgaa": [215, 218, 219], "aatgtt": 218, "aatt": 356, "aattaaataa": 113, "aattctggat": 113, "aattg": 504, "aattgccggac": 504, "aattgg": 326, "aauauggauu": 113, "ab": [115, 200], "ab07acbb1e496801937adfa772424bf7": 491, "ababacac": 200, "abbrevi": [125, 328], "abc": [111, 174, 200, 214, 233, 483], "abcd": 481, "abcdef": 1, "abil": [119, 497], "abl": [20, 24, 88, 189, 220, 226, 233, 264, 347, 411, 425], "about": [1, 30, 34, 67, 96, 97, 99, 100, 111, 114, 115, 119, 123, 124, 126, 151, 154, 160, 162, 163, 165, 176, 179, 186, 188, 191, 195, 223, 225, 228, 232, 248, 251, 259, 290, 296, 301, 303, 327, 330, 332, 341, 347, 348, 356, 386, 391, 406, 498, 499, 503], "abov": [0, 1, 3, 29, 49, 114, 116, 120, 121, 122, 123, 124, 126, 128, 130, 189, 220, 226, 233, 282, 304, 306, 308, 312, 459, 461, 499], "absenc": [48, 348, 388, 436], "absent": [250, 339], "absolut": [261, 269, 306, 396, 476, 490], "abstract": [163, 165, 174, 177, 200, 214], "abund": [1, 43, 44, 45, 53, 55, 58, 60, 67, 71, 81, 83, 85, 86, 87, 88, 91, 108, 264, 269, 327, 333, 334, 340, 341, 348, 390, 396], "abx": 346, "ac": [20, 22, 24, 27, 29, 31, 32, 35, 38, 113, 115, 116, 124, 152, 206, 499], "aca": [241, 242], "acaatcaaat": 113, "acac": [208, 241], "acacatttatta": 242, "acacgacgtt": [209, 239, 241], "acad": [37, 40], "academ": 46, "academi": 253, "acagaattga": 113, "acaggttggc": [114, 121], "acata": 115, "acatggcaat": 113, "acatgggata": 113, "acc": [0, 110, 499], "accaatattt": 113, "accaatttga": 113, "acccc": 0, "acceler": [349, 436], "accept": [1, 20, 31, 88, 193, 194, 230, 231, 249, 253, 258, 264, 306, 310, 312, 344, 347, 348, 427, 430, 456, 457, 463, 471, 474, 495], "acces": 109, "access": [11, 20, 107, 113, 114, 116, 125, 174, 175, 177, 178, 179, 196, 282, 481, 488], "accgaat": 189, "accgaau": 226, "accgggta": 499, "accggttggc": 114, "accggttggccgttcagggtacaggttggccgttcagggtaa": 114, "accgttcg": 124, "accgttgta": [111, 121], "accguuaguc": 499, "accident": 503, "accommod": 152, "accompani": [114, 283, 503], "accomplish": [1, 261, 497], "accord": [49, 53, 189, 220, 226, 338, 342, 394, 395, 479], "accordingli": [476, 478], "account": [49, 95, 213, 318, 333, 341, 348, 502], "accu_dist": 416, "accumul": [63, 66, 409, 416], "accumulate_to_ancestor": [416, 426], "accur": [49, 55, 61, 62, 479, 482], "accuraci": [308, 339], "acdefghikl": [95, 98], "acdfnasanftacgnpnrtesl": 240, "acg": [20, 27, 28, 29, 31, 32, 122, 124, 239, 241], "acga": [20, 21, 24, 233], "acgaactatt": 113, "acggggaggcggag": [190, 205, 221, 227], "acgggu": 499, "acgt": [20, 21, 24, 25, 33, 174, 175, 177, 178, 216, 217, 218, 233, 234, 243, 252, 256], "acgta": 122, "acgtac": 122, "acgtacgt": 216, "acgtgagctacaaaag": 115, "acgtgccta": 0, "acgtgcctaggtacgcaag": 0, "acgtggaa": 234, "acgtn": 250, "acgtu": 42, "achiev": [71, 459, 460, 467, 476, 499], "acid": [35, 37, 40, 113, 114, 115, 118, 121, 125, 189, 196, 198, 200, 220, 226, 233, 250, 252, 253], "acquir": 347, "across": [7, 27, 71, 114, 115, 121, 154, 185, 264, 269, 306, 347, 357, 461, 480], "act": [0, 29, 128, 129, 130], "actaaggctc": 0, "actaaggctcctaacccccttttctcaga": 0, "actaaggctctct": 0, "actaaggctctctacccctctcagaga": 0, "actacattcg": 113, "actatacgga": 113, "actcat": 114, "action": 165, "activ": 496, "acttagtt": 216, "actual": [72, 78, 123, 126, 139, 306], "acwgn": [201, 203, 211], "ad": [19, 35, 36, 37, 38, 39, 40, 114, 124, 155, 214, 233, 264, 269, 334, 337, 356, 381, 411, 415, 416, 417, 421, 427, 436, 439, 440, 441, 450, 454, 455, 456, 457, 459, 460, 461, 462, 473, 474, 475, 476, 478, 492, 502], "adapt": 480, "adata": 398, "add": [1, 36, 39, 123, 124, 126, 132, 152, 154, 156, 158, 233, 266, 273, 274, 276, 277, 278, 351, 352, 356, 376, 397, 411, 425, 427], "add_format": [128, 130], "addit": [1, 41, 42, 53, 84, 85, 86, 90, 113, 114, 115, 116, 117, 121, 122, 123, 179, 189, 220, 226, 252, 261, 262, 263, 264, 282, 297, 408, 415, 427, 428, 429, 480, 492, 497], "addition": [1, 20, 108, 119, 148, 154, 395, 475, 499, 502], "additon": 114, "address": [264, 497], "adenin": [189, 226], "adequ": 347, "adher": 123, "adiv_faith_pd": 1, "adiv_sob": 1, "adjac": [240, 365], "adjust": 71, "adoni": 307, "adopt": [71, 250], "advanc": [1, 20], "advantag": [71, 297, 492], "advis": [85, 86, 91], "ae000111": 110, "ae000171": 110, "ae000174": 110, "ae000394": 110, "ae000425": 110, "af031394": 110, "af035635": 124, "af178031": 110, "af178032": 110, "af178033": 110, "affect": [114, 119, 196, 233, 304, 308, 475], "aforement": 125, "after": [19, 21, 24, 35, 36, 37, 114, 115, 123, 124, 125, 126, 154, 158, 185, 269, 275, 276, 305, 306, 309, 312, 333, 348, 423, 452, 454, 462, 472], "ag": [20, 21, 24, 27, 282, 346, 347], "agaagacc": 238, "agaagctatg": 113, "agaagctctt": 113, "agaagcuaug": 113, "agacatcacg": 113, "agagcatgcg": 113, "agaggttcta": 116, "agagguucua": 116, "agagttgaag": 121, "agagttgaaggtatct": [111, 121], "again": [1, 20, 114, 115, 179, 279, 387, 481], "against": [20, 35, 38, 115, 152, 154, 196, 233, 264, 312, 354, 355, 418], "agatataaag": 113, "agatcttttg": 113, "agatgagtat": 113, "agctttctgc": 113, "agg": 499, "aggaccttat": 113, "aggctc": 0, "aggctcccttctacccctctcagaga": 0, "agggaaagtt": 113, "agggctggct": 113, "agggga": 499, "agggta": 259, "aggreg": 504, "aggtacccta": 113, "aggtgcagta": 113, "agre": [140, 144], "agtactctaa": 113, "agtgcagggt": [114, 121], "aguauucugccacuguaagaa": 198, "aguc": [236, 244, 246], "ahead": 504, "aiacaqkm": 124, "aim": 327, "ainsworth": 305, "aitchison": [261, 262, 263, 267, 268, 270, 271, 279], "aitchson": 272, "al": [264, 269, 312, 350, 407], "ala": 220, "alanin": [23, 220], "aldex2": 269, "alexandro": 414, "algorithm": [35, 38, 116, 304, 305, 306, 308, 313, 314, 315, 317, 318, 320, 322, 324, 325, 333, 334, 341, 418, 479, 481, 482, 503], "alia": [11, 51, 53, 68, 69, 71, 77, 85, 86, 117, 252, 264, 274, 291, 417, 440, 444, 446], "alic": 233, "alig": 13, "align": [109, 110, 114, 115, 152, 154, 233, 252, 353, 354, 355, 496, 497, 499], "aligned_query_sequ": [0, 11], "aligned_target_sequ": [0, 11], "alignmentstructur": 19, "alignpath": 14, "all": [1, 19, 20, 22, 23, 29, 35, 36, 37, 42, 44, 53, 54, 55, 67, 71, 72, 78, 81, 83, 85, 86, 87, 88, 103, 104, 105, 106, 107, 109, 111, 112, 113, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 133, 143, 152, 154, 156, 158, 159, 168, 174, 175, 177, 178, 183, 185, 189, 198, 202, 204, 213, 220, 226, 233, 234, 238, 240, 249, 252, 253, 256, 264, 266, 269, 273, 274, 276, 277, 278, 279, 282, 284, 287, 292, 295, 299, 302, 304, 305, 306, 307, 308, 309, 317, 318, 325, 326, 327, 329, 331, 338, 339, 347, 348, 349, 356, 357, 360, 364, 397, 405, 410, 413, 414, 415, 416, 421, 425, 429, 430, 444, 445, 446, 447, 451, 452, 456, 457, 463, 464, 466, 468, 475, 476, 478, 480, 492, 502], "all_char": 119, "allow": [109, 114, 115, 119, 121, 122, 123, 126, 128, 130, 148, 154, 179, 189, 220, 226, 234, 238, 261, 283, 284, 304, 305, 307, 308, 309, 313, 339, 350, 356, 407, 416, 425, 471, 479, 492, 504], "allow_edge_estim": [479, 482], "allow_empti": 471, "allow_overlap": 284, "allvltkt": 124, "almost": 485, "alon": [119, 305], "along": [20, 118, 177, 329, 338, 339, 373, 394, 405], "alpha": [83, 89, 264, 344, 345, 349], "alpha_divers": [1, 43, 53, 71, 87, 89], "alpha_pwr": [344, 347, 348], "alphabet": [0, 32, 42, 89, 90, 109, 114, 189, 196, 200, 220, 226, 233, 250, 252, 253, 254, 256, 259, 499], "alphanumer": 123, "alr": 263, "alreadi": [119, 124, 126, 128, 129, 130, 233, 283, 306, 459, 461, 475], "also": [0, 1, 20, 22, 23, 49, 53, 76, 84, 85, 86, 87, 94, 98, 102, 113, 114, 115, 116, 117, 118, 119, 121, 123, 124, 125, 126, 127, 154, 179, 198, 217, 233, 240, 249, 250, 252, 264, 279, 280, 282, 304, 305, 306, 308, 312, 327, 334, 341, 344, 347, 348, 361, 366, 378, 408, 416, 451, 453, 476, 482, 483, 485, 495, 497, 499, 504], "alter": 503, "altern": [31, 51, 76, 125, 126, 198, 212, 261, 275, 281, 287, 299, 306, 308, 309, 312, 339, 344, 433, 463], "although": [71, 312, 347, 357, 414], "altschul": [109, 110], "alwai": [1, 19, 20, 113, 116, 119, 121, 123, 129, 148, 152, 155, 179, 185, 198, 283, 381, 425, 439, 459, 460, 461, 488, 504], "amar": 116, "ambigu": [141, 145, 189, 214, 226], "amen": 262, "american": [44, 460], "amino": [35, 37, 40, 113, 114, 118, 189, 196, 198, 220, 250, 252, 253], "amino_acid": 196, "among": [1, 49, 71, 104, 116, 295, 314, 334, 341, 500], "amount": [309, 408, 504], "amplicon": [1, 353], "amsterdam": [327, 333, 334, 341], "an": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 31, 34, 35, 36, 37, 41, 51, 53, 54, 56, 64, 67, 68, 69, 73, 74, 77, 82, 83, 85, 86, 87, 91, 97, 100, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 134, 136, 137, 138, 140, 142, 144, 146, 148, 149, 152, 154, 155, 156, 158, 159, 161, 162, 164, 169, 170, 175, 177, 178, 179, 185, 188, 190, 195, 196, 198, 200, 205, 214, 221, 225, 226, 227, 232, 233, 234, 244, 246, 249, 250, 251, 252, 256, 264, 267, 268, 270, 271, 274, 276, 279, 280, 282, 283, 284, 286, 287, 291, 295, 296, 298, 299, 303, 304, 306, 307, 308, 312, 319, 322, 326, 327, 328, 332, 338, 339, 344, 346, 347, 348, 349, 350, 351, 352, 353, 359, 360, 363, 364, 365, 366, 371, 373, 374, 376, 379, 380, 381, 382, 384, 386, 387, 397, 400, 403, 404, 405, 406, 407, 408, 409, 411, 412, 414, 416, 417, 421, 423, 424, 428, 431, 432, 440, 444, 446, 449, 454, 456, 457, 459, 460, 461, 462, 463, 468, 470, 473, 475, 476, 477, 478, 479, 480, 481, 482, 488, 489, 490, 491, 492, 495, 497, 499, 502, 503, 504], "analog": 71, "analogu": 308, "analys": [53, 85, 86, 304, 436, 441, 500], "analysi": [1, 53, 67, 85, 86, 114, 121, 261, 262, 264, 269, 279, 304, 307, 308, 313, 314, 316, 317, 321, 323, 324, 325, 329, 333, 334, 339, 340, 341, 344, 347, 348, 408, 436], "analyt": 54, "analyz": [1, 261, 334, 347], "ancacwwgacgtt": [207, 208, 210], "ancestor": [53, 71, 234, 408, 409, 416, 444, 446, 461], "ancestr": [53, 409], "ancom_df": 264, "anderson": [307, 308], "ani": [1, 10, 19, 20, 22, 23, 29, 31, 41, 42, 45, 80, 81, 114, 116, 118, 119, 123, 124, 128, 129, 130, 141, 145, 148, 152, 154, 158, 159, 167, 179, 181, 184, 189, 220, 226, 233, 252, 259, 264, 266, 269, 306, 309, 313, 318, 322, 333, 338, 344, 346, 347, 361, 366, 390, 400, 402, 408, 411, 414, 416, 417, 423, 427, 435, 436, 437, 439, 440, 455, 468, 470, 480, 492, 493, 495, 502, 504], "anim": 54, "ann": [52, 74], "anndata": 398, "annot": [113, 116, 117, 123, 154], "announc": 123, "anosim": [1, 307, 308], "anoth": [1, 20, 21, 29, 53, 85, 86, 116, 118, 119, 152, 154, 158, 161, 165, 179, 196, 233, 236, 245, 247, 252, 283, 312, 353, 411, 426], "anova": [264, 307, 315, 319], "answer": 491, "anti": [1, 304], "antibiot": [276, 346], "anticip": 504, "anyon": 123, "anyth": [1, 114, 115, 122, 126, 233, 400, 492, 493, 495, 504], "anytim": 123, "anywher": [118, 119, 123, 264], "apart": 460, "api": [114, 179, 258], "app": 122, "appear": [1, 44, 109, 121, 123, 124, 286, 305, 333, 334, 339, 344, 350, 475, 483], "append": [0, 24, 121, 126, 233, 427, 439], "appl": [85, 86], "appli": [0, 1, 19, 20, 23, 83, 86, 87, 88, 91, 113, 114, 119, 123, 125, 154, 165, 174, 175, 177, 178, 189, 220, 226, 233, 252, 261, 287, 299, 300, 306, 309, 313, 333, 347, 360, 381, 387, 390, 396, 403, 411, 416, 421, 427, 439, 481, 492, 504], "applic": [19, 23, 35, 41, 179, 327, 416, 420, 462, 504], "approach": [269, 306, 347, 421, 424], "appropri": [1, 107, 118, 148, 234, 264, 497, 502], "approx": 344, "approxim": [341, 344], "aqfvdhwkel": 112, "aquat": 334, "ar": [0, 1, 3, 19, 20, 22, 23, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 47, 48, 49, 53, 54, 60, 61, 62, 71, 83, 85, 86, 87, 88, 90, 91, 96, 97, 99, 100, 103, 104, 105, 106, 107, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 128, 129, 130, 133, 140, 143, 144, 148, 152, 154, 156, 158, 160, 161, 162, 165, 167, 168, 179, 180, 181, 183, 184, 185, 186, 188, 189, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 204, 207, 208, 209, 210, 215, 220, 222, 223, 225, 226, 228, 229, 230, 231, 232, 233, 234, 238, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 259, 260, 261, 262, 264, 266, 269, 270, 271, 273, 274, 276, 277, 278, 279, 282, 283, 287, 290, 291, 295, 296, 297, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 312, 315, 318, 325, 326, 327, 328, 329, 330, 332, 333, 334, 337, 338, 339, 341, 342, 344, 346, 347, 348, 350, 356, 357, 360, 362, 366, 372, 381, 383, 391, 393, 394, 395, 396, 398, 399, 400, 405, 406, 407, 408, 413, 414, 416, 418, 421, 423, 433, 436, 439, 441, 447, 448, 449, 455, 456, 457, 459, 460, 461, 462, 463, 464, 468, 469, 470, 471, 472, 475, 476, 478, 480, 482, 483, 485, 486, 488, 489, 492, 494, 495, 497, 499, 502, 503, 504], "arang": [372, 377], "arbitrari": [20, 22, 25, 118, 123, 124, 189, 220, 226, 233, 326, 366, 400, 492, 499], "arbitrarili": [480, 504], "archaea": [433, 434, 471], "archiv": [125, 491], "area": [1, 55], "arg": [126, 133, 143, 193, 194, 220, 230, 231, 350], "arginin": 220, "argument": [19, 20, 30, 31, 34, 41, 96, 97, 99, 100, 118, 128, 129, 130, 133, 140, 141, 142, 143, 144, 145, 146, 160, 162, 186, 188, 191, 193, 194, 195, 223, 225, 228, 230, 231, 232, 243, 248, 251, 252, 262, 287, 290, 296, 299, 301, 303, 310, 330, 332, 350, 391, 406, 416, 492, 495], "argumentoverridewarn": [140, 144], "aris": [470, 480], "arithmet": 483, "around": [61, 62, 88, 114, 121, 124, 252, 265, 306, 345, 502], "arrai": [1, 3, 4, 5, 6, 8, 9, 10, 15, 17, 19, 23, 27, 53, 71, 85, 86, 94, 95, 98, 102, 105, 114, 120, 189, 201, 203, 206, 211, 215, 219, 220, 224, 226, 233, 245, 247, 250, 252, 254, 256, 262, 263, 265, 266, 267, 268, 270, 271, 272, 273, 275, 276, 277, 278, 279, 280, 282, 283, 291, 298, 312, 313, 318, 322, 325, 327, 338, 342, 344, 345, 346, 347, 348, 349, 353, 354, 355, 356, 357, 359, 360, 373, 376, 380, 384, 386, 390, 392, 396, 397, 400, 403, 416, 438, 470, 480, 499], "arrang": 327, "array_lik": [1, 3, 4, 5, 6, 14, 15, 16, 20, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 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134, 136, 137, 138, 200, 488], "clade": [408, 411, 416, 454, 455, 456, 457, 461, 462, 465, 480, 502], "cladogenesi": 312, "claim": [141, 145], "clarifi": 53, "clariti": 119, "clark": [304, 305], "class": [3, 11, 14, 19, 20, 42, 44, 47, 92, 94, 95, 98, 101, 102, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 127, 128, 130, 131, 134, 136, 137, 138, 139, 151, 152, 154, 163, 165, 174, 175, 176, 177, 178, 179, 189, 196, 200, 214, 220, 226, 233, 234, 252, 264, 283, 297, 314, 315, 317, 318, 320, 322, 324, 325, 328, 350, 361, 364, 387, 402, 407, 408, 416, 480, 484, 488, 492, 494, 495, 497], "classic": 125, "classif": [125, 329], "classmethod": [4, 5, 6, 7, 15, 16, 25, 26, 30, 96, 99, 156, 160, 184, 186, 191, 197, 223, 228, 234, 248, 253, 254, 255, 256, 287, 290, 299, 301, 330, 366, 367, 391, 432, 433, 434], "classproperti": 200, "claus": 183, "clean": [148, 454], "clear": [122, 411, 415, 427, 436, 439, 450, 454, 455, 456, 457, 459, 460, 461, 462, 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class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.embl</span></code>)", "FASTA/QUAL format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.fasta</span></code>)", "FASTQ format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.fastq</span></code>)", "GenBank format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.genbank</span></code>)", "GFF3 format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.gff3</span></code>)", "Labeled square matrix format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.lsmat</span></code>)", "Newick format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.newick</span></code>)", "Ordination results format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.ordination</span></code>)", "PHYLIP multiple sequence alignment format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.phylip</span></code>)", "QSeq format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.qseq</span></code>)", "Format Support", "Stockholm format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.stockholm</span></code>)", "Taxdump format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.taxdump</span></code>)", "I/O Registry (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.registry</span></code>)", "skbio.io.registry.Format", "skbio.io.registry.Format.reader", "skbio.io.registry.Format.sniffer", "skbio.io.registry.Format.writer", "skbio.io.registry.IORegistry", "skbio.io.registry.IORegistry.add_format", "skbio.io.registry.IORegistry.create_format", "skbio.io.registry.IORegistry.get_reader", "skbio.io.registry.IORegistry.get_sniffer", "skbio.io.registry.IORegistry.get_writer", "skbio.io.registry.IORegistry.list_read_formats", "skbio.io.registry.IORegistry.list_write_formats", "skbio.io.registry.IORegistry.monkey_patch", "skbio.io.registry.IORegistry.read", "skbio.io.registry.IORegistry.sniff", "skbio.io.registry.IORegistry.write", "skbio.io.registry.create_format", "skbio.io.registry.read", "skbio.io.registry.sniff", "skbio.io.registry.write", "I/O utilities (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.util</span></code>)", "skbio.io.util.open", "skbio.io.util.open_file", "skbio.io.util.open_files", "skbio.metadata.CategoricalMetadataColumn", "skbio.metadata.Interval", "skbio.metadata.Interval.drop", "skbio.metadata.IntervalMetadata", "skbio.metadata.IntervalMetadata.add", "skbio.metadata.IntervalMetadata.concat", "skbio.metadata.IntervalMetadata.drop", "skbio.metadata.IntervalMetadata.merge", "skbio.metadata.IntervalMetadata.query", "skbio.metadata.IntervalMetadata.read", "skbio.metadata.IntervalMetadata.sort", "skbio.metadata.IntervalMetadata.write", "skbio.metadata.IntervalMetadataMixin", "skbio.metadata.IntervalMetadataMixin.has_interval_metadata", "skbio.metadata.MetadataColumn", "skbio.metadata.MetadataColumn.drop_missing_values", "skbio.metadata.MetadataColumn.filter_ids", "skbio.metadata.MetadataColumn.get_ids", "skbio.metadata.MetadataColumn.get_missing", "skbio.metadata.MetadataColumn.get_value", "skbio.metadata.MetadataColumn.has_missing_values", "skbio.metadata.MetadataColumn.to_dataframe", "skbio.metadata.MetadataColumn.to_series", "skbio.metadata.MetadataMixin", "skbio.metadata.MetadataMixin.has_metadata", "skbio.metadata.NumericMetadataColumn", "skbio.metadata.PositionalMetadataMixin", "skbio.metadata.PositionalMetadataMixin.has_positional_metadata", "skbio.metadata.SampleMetadata", "skbio.metadata.SampleMetadata.filter_columns", "skbio.metadata.SampleMetadata.filter_ids", "skbio.metadata.SampleMetadata.get_column", "skbio.metadata.SampleMetadata.get_ids", "skbio.metadata.SampleMetadata.load", "skbio.metadata.SampleMetadata.merge", "skbio.metadata.SampleMetadata.read", "skbio.metadata.SampleMetadata.to_dataframe", "skbio.metadata.SampleMetadata.write", "skbio.sequence.DNA", "skbio.sequence.DNA.find_motifs", "skbio.sequence.DNA.read", "skbio.sequence.DNA.transcribe", "skbio.sequence.DNA.translate", "skbio.sequence.DNA.translate_six_frames", "skbio.sequence.DNA.write", "skbio.sequence.GeneticCode", "skbio.sequence.GeneticCode.from_ncbi", "skbio.sequence.GeneticCode.translate", "skbio.sequence.GeneticCode.translate_six_frames", "skbio.sequence.GrammaredSequence", "skbio.sequence.GrammaredSequence.definites", "skbio.sequence.GrammaredSequence.degap", "skbio.sequence.GrammaredSequence.degenerates", "skbio.sequence.GrammaredSequence.expand_degenerates", "skbio.sequence.GrammaredSequence.find_motifs", "skbio.sequence.GrammaredSequence.gaps", "skbio.sequence.GrammaredSequence.has_definites", "skbio.sequence.GrammaredSequence.has_degenerates", "skbio.sequence.GrammaredSequence.has_gaps", "skbio.sequence.GrammaredSequence.has_nondegenerates", "skbio.sequence.GrammaredSequence.nondegenerates", "skbio.sequence.GrammaredSequence.to_definites", "skbio.sequence.GrammaredSequence.to_regex", "skbio.sequence.NucleotideMixin", "skbio.sequence.NucleotideMixin.complement", "skbio.sequence.NucleotideMixin.gc_content", "skbio.sequence.NucleotideMixin.gc_frequency", "skbio.sequence.NucleotideMixin.is_reverse_complement", "skbio.sequence.NucleotideMixin.reverse_complement", "skbio.sequence.Protein", "skbio.sequence.Protein.find_motifs", "skbio.sequence.Protein.has_stops", "skbio.sequence.Protein.read", "skbio.sequence.Protein.stops", "skbio.sequence.Protein.write", "skbio.sequence.RNA", "skbio.sequence.RNA.find_motifs", "skbio.sequence.RNA.read", "skbio.sequence.RNA.reverse_transcribe", "skbio.sequence.RNA.translate", "skbio.sequence.RNA.translate_six_frames", "skbio.sequence.RNA.write", "skbio.sequence.Sequence", "skbio.sequence.Sequence.concat", "skbio.sequence.Sequence.count", "skbio.sequence.Sequence.distance", "skbio.sequence.Sequence.find_with_regex", "skbio.sequence.Sequence.frequencies", "skbio.sequence.Sequence.index", "skbio.sequence.Sequence.iter_contiguous", "skbio.sequence.Sequence.iter_kmers", "skbio.sequence.Sequence.kmer_frequencies", "skbio.sequence.Sequence.lowercase", "skbio.sequence.Sequence.match_frequency", "skbio.sequence.Sequence.matches", "skbio.sequence.Sequence.mismatch_frequency", "skbio.sequence.Sequence.mismatches", "skbio.sequence.Sequence.read", "skbio.sequence.Sequence.replace", "skbio.sequence.Sequence.to_indices", "skbio.sequence.Sequence.write", "skbio.sequence.SubstitutionMatrix", "skbio.sequence.SubstitutionMatrix.by_name", "skbio.sequence.SubstitutionMatrix.from_dict", "skbio.sequence.SubstitutionMatrix.get_names", "skbio.sequence.SubstitutionMatrix.identity", "skbio.sequence.SubstitutionMatrix.to_dict", "Sequence distance metrics (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.sequence.distance</span></code>)", "skbio.sequence.distance.hamming", "skbio.sequence.distance.kmer_distance", "Composition Statistics (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.stats.composition</span></code>)", "skbio.stats.composition.alr", "skbio.stats.composition.alr_inv", "skbio.stats.composition.ancom", "skbio.stats.composition.centralize", "skbio.stats.composition.closure", "skbio.stats.composition.clr", "skbio.stats.composition.clr_inv", "skbio.stats.composition.dirmult_ttest", "skbio.stats.composition.ilr", "skbio.stats.composition.ilr_inv", "skbio.stats.composition.inner", "skbio.stats.composition.multi_replace", "skbio.stats.composition.multiplicative_replacement", "skbio.stats.composition.pairwise_vlr", "skbio.stats.composition.perturb", "skbio.stats.composition.perturb_inv", "skbio.stats.composition.power", "skbio.stats.composition.sbp_basis", "skbio.stats.composition.tree_basis", "skbio.stats.composition.vlr", "Distance matrix-based statistics (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.stats.distance</span></code>)", "skbio.stats.distance.DissimilarityMatrix", "skbio.stats.distance.DissimilarityMatrix.between", "skbio.stats.distance.DissimilarityMatrix.copy", "skbio.stats.distance.DissimilarityMatrix.filter", "skbio.stats.distance.DissimilarityMatrix.from_iterable", "skbio.stats.distance.DissimilarityMatrix.index", "skbio.stats.distance.DissimilarityMatrix.plot", "skbio.stats.distance.DissimilarityMatrix.read", "skbio.stats.distance.DissimilarityMatrix.redundant_form", "skbio.stats.distance.DissimilarityMatrix.rename", "skbio.stats.distance.DissimilarityMatrix.to_data_frame", "skbio.stats.distance.DissimilarityMatrix.transpose", "skbio.stats.distance.DissimilarityMatrix.within", "skbio.stats.distance.DissimilarityMatrix.write", "skbio.stats.distance.DistanceMatrix", "skbio.stats.distance.DistanceMatrix.condensed_form", "skbio.stats.distance.DistanceMatrix.from_iterable", "skbio.stats.distance.DistanceMatrix.permute", "skbio.stats.distance.DistanceMatrix.read", "skbio.stats.distance.DistanceMatrix.to_series", "skbio.stats.distance.DistanceMatrix.write", "skbio.stats.distance.anosim", "skbio.stats.distance.bioenv", "skbio.stats.distance.mantel", "skbio.stats.distance.permanova", "skbio.stats.distance.permdisp", "skbio.stats.distance.pwmantel", "skbio.stats.distance.randdm", "Evolutionary statistics (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.stats.evolve</span></code>)", "skbio.stats.evolve.hommola_cospeciation", "Gradient analyses (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.stats.gradient</span></code>)", "skbio.stats.gradient.AverageGradientANOVA", "skbio.stats.gradient.CategoryResults", "skbio.stats.gradient.CategoryResults.to_files", "skbio.stats.gradient.FirstDifferenceGradientANOVA", "skbio.stats.gradient.GradientANOVA", "skbio.stats.gradient.GradientANOVA.get_trajectories", "skbio.stats.gradient.GradientANOVAResults", "skbio.stats.gradient.GradientANOVAResults.to_files", "skbio.stats.gradient.GroupResults", "skbio.stats.gradient.GroupResults.to_files", "skbio.stats.gradient.TrajectoryGradientANOVA", "skbio.stats.gradient.WindowDifferenceGradientANOVA", "skbio.stats.isubsample", "Ordination methods (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.stats.ordination</span></code>)", "skbio.stats.ordination.OrdinationResults", "skbio.stats.ordination.OrdinationResults.plot", "skbio.stats.ordination.OrdinationResults.read", "skbio.stats.ordination.OrdinationResults.rename", "skbio.stats.ordination.OrdinationResults.write", "skbio.stats.ordination.ca", "skbio.stats.ordination.cca", "skbio.stats.ordination.corr", "skbio.stats.ordination.e_matrix", "skbio.stats.ordination.f_matrix", "skbio.stats.ordination.mean_and_std", "skbio.stats.ordination.pcoa", "skbio.stats.ordination.pcoa_biplot", "skbio.stats.ordination.rda", "skbio.stats.ordination.scale", "skbio.stats.ordination.svd_rank", "Empirical Power Estimation (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.stats.power</span></code>)", "skbio.stats.power.confidence_bound", "skbio.stats.power.paired_subsamples", "skbio.stats.power.subsample_paired_power", "skbio.stats.power.subsample_power", "skbio.stats.subsample_counts", "skbio.table.Table", "skbio.table.Table.add_group_metadata", "skbio.table.Table.add_metadata", "skbio.table.Table.align_to", "skbio.table.Table.align_to_dataframe", "skbio.table.Table.align_tree", "skbio.table.Table.collapse", "skbio.table.Table.concat", "skbio.table.Table.copy", "skbio.table.Table.data", "skbio.table.Table.del_metadata", "skbio.table.Table.delimited_self", "skbio.table.Table.descriptive_equality", "skbio.table.Table.exists", "skbio.table.Table.filter", "skbio.table.Table.from_adjacency", "skbio.table.Table.from_hdf5", "skbio.table.Table.from_json", "skbio.table.Table.from_tsv", "skbio.table.Table.get_table_density", "skbio.table.Table.get_value_by_ids", "skbio.table.Table.group_metadata", "skbio.table.Table.head", "skbio.table.Table.ids", "skbio.table.Table.index", "skbio.table.Table.is_empty", "skbio.table.Table.iter", "skbio.table.Table.iter_data", "skbio.table.Table.iter_pairwise", "skbio.table.Table.length", "skbio.table.Table.max", "skbio.table.Table.merge", "skbio.table.Table.metadata", "skbio.table.Table.metadata_to_dataframe", "skbio.table.Table.min", "skbio.table.Table.nonzero", "skbio.table.Table.nonzero_counts", "skbio.table.Table.norm", "skbio.table.Table.pa", "skbio.table.Table.partition", "skbio.table.Table.rankdata", "skbio.table.Table.read", "skbio.table.Table.reduce", "skbio.table.Table.remove_empty", "skbio.table.Table.sort", "skbio.table.Table.sort_order", "skbio.table.Table.subsample", "skbio.table.Table.sum", "skbio.table.Table.to_anndata", "skbio.table.Table.to_dataframe", "skbio.table.Table.to_hdf5", "skbio.table.Table.to_json", "skbio.table.Table.to_tsv", "skbio.table.Table.transform", "skbio.table.Table.transpose", "skbio.table.Table.update_ids", "skbio.table.Table.write", "skbio.table.example_table", "skbio.tree.TreeNode", "skbio.tree.TreeNode.accumulate_to_ancestor", "skbio.tree.TreeNode.ancestors", "skbio.tree.TreeNode.append", "skbio.tree.TreeNode.ascii_art", "skbio.tree.TreeNode.assign_ids", "skbio.tree.TreeNode.assign_supports", "skbio.tree.TreeNode.bifurcate", "skbio.tree.TreeNode.cache_attr", "skbio.tree.TreeNode.clear_caches", "skbio.tree.TreeNode.compare_rfd", "skbio.tree.TreeNode.compare_subsets", "skbio.tree.TreeNode.compare_tip_distances", "skbio.tree.TreeNode.copy", "skbio.tree.TreeNode.count", "skbio.tree.TreeNode.create_caches", "skbio.tree.TreeNode.deepcopy", "skbio.tree.TreeNode.descending_branch_length", "skbio.tree.TreeNode.distance", "skbio.tree.TreeNode.extend", "skbio.tree.TreeNode.find", "skbio.tree.TreeNode.find_all", "skbio.tree.TreeNode.find_by_func", "skbio.tree.TreeNode.find_by_id", "skbio.tree.TreeNode.from_linkage_matrix", "skbio.tree.TreeNode.from_taxdump", "skbio.tree.TreeNode.from_taxonomy", "skbio.tree.TreeNode.get_max_distance", "skbio.tree.TreeNode.has_caches", "skbio.tree.TreeNode.has_children", "skbio.tree.TreeNode.index_tree", "skbio.tree.TreeNode.insert", "skbio.tree.TreeNode.invalidate_caches", "skbio.tree.TreeNode.is_bifurcating", "skbio.tree.TreeNode.is_root", "skbio.tree.TreeNode.is_tip", "skbio.tree.TreeNode.lca", "skbio.tree.TreeNode.levelorder", "skbio.tree.TreeNode.lowest_common_ancestor", "skbio.tree.TreeNode.neighbors", "skbio.tree.TreeNode.non_tips", "skbio.tree.TreeNode.observed_node_counts", "skbio.tree.TreeNode.pop", "skbio.tree.TreeNode.postorder", "skbio.tree.TreeNode.pre_and_postorder", "skbio.tree.TreeNode.preorder", "skbio.tree.TreeNode.prune", "skbio.tree.TreeNode.remove", "skbio.tree.TreeNode.remove_by_func", "skbio.tree.TreeNode.remove_deleted", "skbio.tree.TreeNode.root", "skbio.tree.TreeNode.root_at", "skbio.tree.TreeNode.root_at_midpoint", "skbio.tree.TreeNode.root_by_outgroup", "skbio.tree.TreeNode.shear", "skbio.tree.TreeNode.shuffle", "skbio.tree.TreeNode.siblings", "skbio.tree.TreeNode.subset", "skbio.tree.TreeNode.subsets", "skbio.tree.TreeNode.subtree", "skbio.tree.TreeNode.tip_tip_distances", "skbio.tree.TreeNode.tips", "skbio.tree.TreeNode.to_array", "skbio.tree.TreeNode.to_taxonomy", "skbio.tree.TreeNode.traverse", "skbio.tree.TreeNode.unpack", "skbio.tree.TreeNode.unpack_by_func", "skbio.tree.TreeNode.unroot", "skbio.tree.TreeNode.unrooted_copy", "skbio.tree.TreeNode.unrooted_deepcopy", "skbio.tree.TreeNode.unrooted_move", "skbio.tree.gme", "skbio.tree.majority_rule", "skbio.tree.nj", "skbio.tree.nni", "skbio.tree.upgma", "skbio.util.PlottableMixin", "skbio.util.assert_data_frame_almost_equal", "skbio.util.assert_ordination_results_equal", "skbio.util.cardinal_to_ordinal", "skbio.util.classproperty", "skbio.util.find_duplicates", "skbio.util.get_data_path", "skbio.util.safe_md5", "skbio.workflow.Workflow", "skbio.workflow.Workflow.initialize_state", "skbio.workflow.method", "skbio.workflow.requires", "Home", "Input and Output (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io</span></code>)", "Metadata (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.metadata</span></code>)", "Biological Sequences (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.sequence</span></code>)", "Multivariate Statistics (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.stats</span></code>)", "Data Table (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.table</span></code>)", "Trees and Phylogenetics (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.tree</span></code>)", "Utilities for Developers (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.util</span></code>)", "Workflow construction (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.workflow</span></code>)"], "titleterms": {"0": 496, "3": 496, "6": [109, 496], "7": 110, "abstract": [498, 499], "ac": 44, "accumulate_to_ancestor": 409, "ad": 119, "add": 155, "add_format": 132, "add_group_metadata": 351, "add_metadata": 352, "advanc": 119, "algorithm": 0, "align": [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 111, 121, 124], "align_to": 353, "align_to_datafram": 354, "align_tre": 355, "alignmentstructur": [11, 12, 13], "alignpath": [3, 4, 5, 6, 7, 8, 9, 10], "alpha": [1, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82], "alpha_divers": 83, "alr": 262, "alr_inv": 263, "analys": 313, "analysi": 327, "ancestor": 410, "ancom": 264, "anosim": 304, "append": [21, 411], "applic": 119, "argument": 126, "ascii_art": 412, "assert_data_frame_almost_equ": 485, "assert_ordination_results_equ": 486, "assign_id": 413, "assign_support": 414, "averagegradientanova": 314, "base": 282, "basic": 119, "befor": [113, 116], "berger_parker_d": 45, "beta": [1, 84, 85, 86], "beta_divers": 87, "between": 284, "bifurc": 415, "binari": 107, "binary_dm": 107, "bio": [126, 496, 497], "bioenv": 305, "biolog": [2, 499], "biom": [108, 501], "blast": [109, 110], "blast6": 109, "blast7": 110, "block_beta_divers": 88, "brillouin_d": 46, "by_nam": 253, "byte": 93, "ca": 333, "cache_attr": 416, "calcul": 499, "can": 497, "canon": 327, "cardinal_to_ordin": 487, "categor": 282, "categoricalmetadatacolumn": 151, "categoryresult": [315, 316], "caveat": 119, "cca": 334, "central": 265, "chao1": 47, "chao1_ci": 48, "charact": 123, "class": [126, 282, 313, 498, 499, 504], "classproperti": 488, "clear_cach": 417, "closur": 266, "clr": 267, "clr_inv": 268, "clustal": 111, "collaps": 356, "column": [109, 110, 123, 498], "comment": [119, 123], "commun": 1, "compare_rfd": 418, "compare_subset": 419, "compare_tip_dist": 420, "comparison": 282, "complement": 215, "composit": [261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 500], "concat": [156, 234, 357], "condensed_form": 298, "confidence_bound": 345, "consensu": 22, "conserv": 23, "construct": 504, "continu": 282, "cophylogenet": 311, "copi": [285, 358, 421], "corr": 335, "correspond": 327, "count": [1, 235, 422], "coverag": 43, "creat": 126, "create_cach": 423, "create_format": [133, 143], "custom": 497, "data": [0, 114, 282, 359, 500, 501], "decor": 504, "deepcopi": 424, "definit": 201, "degap": 202, "degener": 203, "del_metadata": 360, "delimited_self": 361, "deprec": 0, "descending_branch_length": 425, "descriptive_equ": 362, "detail": 503, "dev": 496, "develop": [497, 503], "dirmult_ttest": 269, "dissimilar": 107, "dissimilaritymatrix": [283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296], "distanc": [236, 258, 259, 260, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 426, 499, 500], "distancematrix": [297, 298, 299, 300, 301, 302, 303], "divers": [1, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 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113, "file": [113, 114, 116, 497], "filter": [286, 364], "filter_column": 180, "filter_id": [167, 181], "find": 428, "find_al": 429, "find_by_func": 430, "find_by_id": 431, "find_dupl": 489, "find_motif": [190, 205, 221, 227], "find_with_regex": 237, "firstdifferencegradientanova": 317, "fisher_alpha": 54, "footer": 124, "formal": 119, "format": [107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 497], "frequenc": 238, "from": 497, "from_adjac": 365, "from_bit": [4, 15], "from_cigar": 16, "from_coordin": 5, "from_dict": [25, 254], "from_hdf5": 366, "from_indic": 6, "from_iter": [287, 299], "from_json": 367, "from_linkage_matrix": 432, "from_ncbi": 197, "from_path_seq": 26, "from_tabular": 7, "from_taxdump": 433, "from_taxonomi": 434, "from_tsv": 368, "ft": 113, "function": [0, 84, 126, 147, 258, 261, 282, 311, 327, 344], "g": 124, "gap": 206, "gap_frequ": 27, "gc": 124, "gc_content": 216, "gc_frequenc": 217, 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"aaacccttgc": [114, 121], "aaacccttgccg": 114, "aaacccttgccggtacgcttaaaccattgccggtacgcttaa": 114, "aaacccttgccgttacgcttaaaccgaggccgggacactcat": 114, "aaaccgaggc": [114, 121], "aaagataggc": 113, "aaatatggat": 113, "aaatcctatg": 113, "aac": 122, "aacaaatgca": 113, "aacaacagga": 113, "aacaccaaacttctccacc": 115, "aacaccaaacttctccaccacgtgagctacaaaag": 115, "aaccttatca": 113, "aacga": 233, "aacgaaggcg": 113, "aacgac": 233, "aactttgtag": 113, "aagaactttc": 113, "aagaggttac": 113, "aagcctggtg": 113, "aagccttggc": 114, "aagccttggcagtgcagggtgagccgtgg": 114, "aagccttggcagtgcagggtgagccgtggccgggcacggtat": 114, "aagctngggc": [114, 121], "aagctngggcatttcagggtgagcccgggcaatacagggtat": 114, "aagga": 233, "aaggaatcaa": 113, "aaggaatttg": 113, "aagtaa": 215, "aagtatttgg": 113, "aagtcttaga": 113, "aagtcttttt": 113, "aagttgttag": 113, "aagucuuuuu": 113, "aata": 122, "aataaac": 122, "aataagtgca": 113, "aatacagggt": [114, 121], "aatataccggttataa": 237, "aatatggatt": 113, "aatgaa": [215, 218, 219], "aatgtt": 218, "aatt": 356, "aattaaataa": 113, "aattctggat": 113, "aattg": 504, "aattgccggac": 504, "aattgg": 326, "aauauggauu": 113, "ab": [115, 200], "ab07acbb1e496801937adfa772424bf7": 491, "ababacac": 200, "abbrevi": [125, 328], "abc": [111, 174, 200, 214, 233, 483], "abcd": 481, "abcdef": 1, "abil": [119, 497], "abl": [20, 24, 88, 189, 220, 226, 233, 264, 347, 411, 425], "about": [1, 30, 34, 67, 96, 97, 99, 100, 111, 114, 115, 119, 123, 124, 126, 151, 154, 160, 162, 163, 165, 176, 179, 186, 188, 191, 195, 223, 225, 228, 232, 248, 251, 259, 290, 296, 301, 303, 327, 330, 332, 341, 347, 348, 356, 386, 391, 406, 498, 499, 503], "abov": [0, 1, 3, 29, 49, 114, 116, 120, 121, 122, 123, 124, 126, 128, 130, 189, 220, 226, 233, 282, 304, 306, 308, 312, 459, 461, 499], "absenc": [48, 348, 388, 436], "absent": [250, 339], "absolut": [261, 269, 306, 396, 476, 490], "abstract": [163, 165, 174, 177, 200, 214], "abund": [1, 43, 44, 45, 53, 55, 58, 60, 67, 71, 81, 83, 85, 86, 87, 88, 91, 108, 264, 269, 327, 333, 334, 340, 341, 348, 390, 396], "abx": 346, "ac": [20, 22, 24, 27, 29, 31, 32, 35, 38, 113, 115, 116, 124, 152, 206, 499], "aca": [241, 242], "acaatcaaat": 113, "acac": [208, 241], "acacatttatta": 242, "acacgacgtt": [209, 239, 241], "acad": [37, 40], "academ": 46, "academi": 253, "acagaattga": 113, "acaggttggc": [114, 121], "acata": 115, "acatggcaat": 113, "acatgggata": 113, "acc": [0, 110, 499], "accaatattt": 113, "accaatttga": 113, "acccc": 0, "acceler": [349, 436], "accept": [1, 20, 31, 88, 193, 194, 230, 231, 249, 253, 258, 264, 306, 310, 312, 344, 347, 348, 420, 427, 430, 456, 457, 463, 471, 474, 495], "acces": 109, "access": [11, 20, 107, 113, 114, 116, 125, 174, 175, 177, 178, 179, 196, 282, 481, 488], "accgaat": 189, "accgaau": 226, "accgggta": 499, "accggttggc": 114, "accggttggccgttcagggtacaggttggccgttcagggtaa": 114, "accgttcg": 124, "accgttgta": [111, 121], "accguuaguc": 499, "accident": 503, "accommod": 152, "accompani": [114, 283, 503], "accomplish": [1, 261, 497], "accord": [49, 53, 189, 220, 226, 338, 342, 394, 395, 479], "accordingli": [476, 478], "account": [49, 95, 213, 318, 333, 341, 348, 502], "accu_dist": 416, "accumul": [63, 66, 409, 416], "accumulate_to_ancestor": [416, 426], "accur": [49, 55, 61, 62, 479, 482], "accuraci": [308, 339], "acdefghikl": [95, 98], "acdfnasanftacgnpnrtesl": 240, "acg": [20, 27, 28, 29, 31, 32, 122, 124, 239, 241], "acga": [20, 21, 24, 233], "acgaactatt": 113, "acggggaggcggag": [190, 205, 221, 227], "acgggu": 499, "acgt": [20, 21, 24, 25, 33, 174, 175, 177, 178, 216, 217, 218, 233, 234, 243, 252, 256], "acgta": 122, "acgtac": 122, "acgtacgt": 216, "acgtgagctacaaaag": 115, "acgtgccta": 0, "acgtgcctaggtacgcaag": 0, "acgtggaa": 234, "acgtn": 250, "acgtu": 42, "achiev": [71, 459, 460, 467, 476, 499], "acid": [35, 37, 40, 113, 114, 115, 118, 121, 125, 189, 196, 198, 200, 220, 226, 233, 250, 252, 253], "acquir": 347, "across": [7, 27, 71, 114, 115, 121, 154, 185, 264, 269, 306, 347, 357, 461, 480], "act": [0, 29, 128, 129, 130], "actaaggctc": 0, "actaaggctcctaacccccttttctcaga": 0, "actaaggctctct": 0, "actaaggctctctacccctctcagaga": 0, "actacattcg": 113, "actatacgga": 113, "actcat": 114, "action": 165, "activ": 496, "acttagtt": 216, "actual": [72, 78, 123, 126, 139, 306], "acwgn": [201, 203, 211], "ad": [19, 35, 36, 37, 38, 39, 40, 114, 124, 155, 214, 233, 264, 269, 334, 337, 356, 381, 411, 415, 416, 417, 421, 427, 436, 439, 440, 441, 450, 454, 455, 456, 457, 459, 460, 461, 462, 473, 474, 475, 476, 478, 492, 502], "adapt": 480, "adata": 398, "add": [1, 36, 39, 123, 124, 126, 132, 152, 154, 156, 158, 233, 266, 273, 274, 276, 277, 278, 351, 352, 356, 376, 397, 411, 425, 427], "add_format": [128, 130], "addit": [1, 41, 42, 53, 84, 85, 86, 90, 113, 114, 115, 116, 117, 121, 122, 123, 179, 189, 220, 226, 252, 261, 262, 263, 264, 282, 297, 408, 415, 427, 428, 429, 480, 492, 497], "addition": [1, 20, 108, 119, 148, 154, 395, 475, 499, 502], "additon": 114, "address": [264, 497], "adenin": [189, 226], "adequ": 347, "adher": 123, "adiv_faith_pd": 1, "adiv_sob": 1, "adjac": [240, 365], "adjust": 71, "adoni": 307, "adopt": [71, 250], "advanc": [1, 20], "advantag": [71, 297, 492], "advis": [85, 86, 91], "ae000111": 110, "ae000171": 110, "ae000174": 110, "ae000394": 110, "ae000425": 110, "af031394": 110, "af035635": 124, "af178031": 110, "af178032": 110, "af178033": 110, "affect": [114, 119, 196, 233, 304, 308, 475], "aforement": 125, "after": [19, 21, 24, 35, 36, 37, 114, 115, 123, 124, 125, 126, 154, 158, 185, 269, 275, 276, 305, 306, 309, 312, 333, 348, 423, 452, 454, 462, 472], "ag": [20, 21, 24, 27, 282, 346, 347], "agaagacc": 238, "agaagctatg": 113, "agaagctctt": 113, "agaagcuaug": 113, "agacatcacg": 113, "agagcatgcg": 113, "agaggttcta": 116, "agagguucua": 116, "agagttgaag": 121, "agagttgaaggtatct": [111, 121], "again": [1, 20, 114, 115, 179, 279, 387, 481], "against": [20, 35, 38, 115, 152, 154, 196, 233, 264, 312, 354, 355, 418], "agatataaag": 113, "agatcttttg": 113, "agatgagtat": 113, "agctttctgc": 113, "agg": 499, "aggaccttat": 113, "aggctc": 0, "aggctcccttctacccctctcagaga": 0, "agggaaagtt": 113, "agggctggct": 113, "agggga": 499, "agggta": 259, "aggreg": 504, "aggtacccta": 113, "aggtgcagta": 113, "agre": [140, 144], "agtactctaa": 113, "agtgcagggt": [114, 121], "aguauucugccacuguaagaa": 198, "aguc": [236, 244, 246], "ahead": 504, "aiacaqkm": 124, "aim": 327, "ainsworth": 305, "aitchison": [261, 262, 263, 267, 268, 270, 271, 279], "aitchson": 272, "al": [264, 269, 312, 350, 407], "ala": 220, "alanin": [23, 220], "aldex2": 269, "alexandro": 414, "algorithm": [35, 38, 116, 304, 305, 306, 308, 313, 314, 315, 317, 318, 320, 322, 324, 325, 333, 334, 341, 418, 479, 481, 482, 503], "alia": [11, 51, 53, 68, 69, 71, 77, 85, 86, 117, 252, 264, 274, 291, 417, 440, 444, 446], "alic": 233, "alig": 13, "align": [109, 110, 114, 115, 152, 154, 233, 252, 353, 354, 355, 496, 497, 499], "aligned_query_sequ": [0, 11], "aligned_target_sequ": [0, 11], "alignmentstructur": 19, "alignpath": 14, "all": [1, 19, 20, 22, 23, 29, 35, 36, 37, 42, 44, 53, 54, 55, 67, 71, 72, 78, 81, 83, 85, 86, 87, 88, 103, 104, 105, 106, 107, 109, 111, 112, 113, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 133, 143, 152, 154, 156, 158, 159, 168, 174, 175, 177, 178, 183, 185, 189, 198, 202, 204, 213, 220, 226, 233, 234, 238, 240, 249, 252, 253, 256, 264, 266, 269, 273, 274, 276, 277, 278, 279, 282, 284, 287, 292, 295, 299, 302, 304, 305, 306, 307, 308, 309, 317, 318, 325, 326, 327, 329, 331, 338, 339, 347, 348, 349, 356, 357, 360, 364, 397, 405, 410, 413, 414, 415, 416, 421, 425, 429, 430, 444, 445, 446, 447, 451, 452, 456, 457, 463, 464, 466, 468, 475, 476, 478, 480, 492, 502], "all_char": 119, "allow": [109, 114, 115, 119, 121, 122, 123, 126, 128, 130, 148, 154, 179, 189, 220, 226, 234, 238, 261, 283, 284, 304, 305, 307, 308, 309, 313, 339, 350, 356, 407, 416, 425, 471, 479, 492, 504], "allow_edge_estim": [479, 482], "allow_empti": 471, "allow_overlap": 284, "allvltkt": 124, "almost": 485, "alon": [119, 305], "along": [20, 118, 177, 329, 338, 339, 373, 394, 405], "alpha": [83, 89, 264, 344, 345, 349], "alpha_divers": [1, 43, 53, 71, 87, 89], "alpha_pwr": [344, 347, 348], "alphabet": [0, 32, 42, 89, 90, 109, 114, 189, 196, 200, 220, 226, 233, 250, 252, 253, 254, 256, 259, 499], "alphanumer": 123, "alr": 263, "alreadi": [119, 124, 126, 128, 129, 130, 233, 283, 306, 459, 461, 475], "also": [0, 1, 20, 22, 23, 49, 53, 76, 84, 85, 86, 87, 94, 98, 102, 113, 114, 115, 116, 117, 118, 119, 121, 123, 124, 125, 126, 127, 154, 179, 198, 217, 233, 240, 249, 250, 252, 264, 279, 280, 282, 304, 305, 306, 308, 312, 327, 334, 341, 344, 347, 348, 361, 366, 378, 408, 416, 451, 453, 476, 482, 483, 485, 495, 497, 499, 504], "alter": 503, "altern": [31, 51, 76, 125, 126, 198, 212, 261, 275, 281, 287, 299, 306, 308, 309, 312, 339, 344, 433], "although": [71, 312, 347, 357, 414], "altschul": [109, 110], "alwai": [1, 19, 20, 113, 116, 119, 121, 123, 129, 148, 152, 155, 179, 185, 198, 283, 381, 425, 439, 459, 460, 461, 488, 504], "amar": 116, "ambigu": [141, 145, 189, 214, 226], "amen": 262, "american": [44, 460], "amino": [35, 37, 40, 113, 114, 118, 189, 196, 198, 220, 250, 252, 253], "amino_acid": 196, "among": [1, 49, 71, 104, 116, 295, 314, 334, 341, 500], "amount": [309, 408, 504], "amplicon": [1, 353], "amsterdam": [327, 333, 334, 341], "an": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 31, 34, 35, 36, 37, 41, 51, 53, 54, 56, 64, 67, 68, 69, 73, 74, 77, 82, 83, 85, 86, 87, 91, 97, 100, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 134, 136, 137, 138, 140, 142, 144, 146, 148, 149, 152, 154, 155, 156, 158, 159, 161, 162, 164, 169, 170, 175, 177, 178, 179, 185, 188, 190, 195, 196, 198, 200, 205, 214, 221, 225, 226, 227, 232, 233, 234, 244, 246, 249, 250, 251, 252, 256, 264, 267, 268, 270, 271, 274, 276, 279, 280, 282, 283, 284, 286, 287, 291, 295, 296, 298, 299, 303, 304, 306, 307, 308, 312, 319, 322, 326, 327, 328, 332, 338, 339, 344, 346, 347, 348, 349, 350, 351, 352, 353, 359, 360, 363, 364, 365, 366, 371, 373, 374, 376, 379, 380, 381, 382, 384, 386, 387, 397, 400, 403, 404, 405, 406, 407, 408, 409, 411, 412, 414, 416, 417, 420, 421, 423, 424, 428, 431, 432, 440, 444, 446, 449, 454, 456, 457, 459, 460, 461, 462, 463, 468, 470, 473, 475, 476, 477, 478, 479, 480, 481, 482, 488, 489, 490, 491, 492, 495, 497, 499, 502, 503, 504], "analog": 71, "analogu": 308, "analys": [53, 85, 86, 304, 436, 441, 500], "analysi": [1, 53, 67, 85, 86, 114, 121, 261, 262, 264, 269, 279, 304, 307, 308, 313, 314, 316, 317, 321, 323, 324, 325, 329, 333, 334, 339, 340, 341, 344, 347, 348, 408, 436], "analyt": 54, "analyz": [1, 261, 334, 347], "ancacwwgacgtt": [207, 208, 210], "ancestor": [53, 71, 234, 408, 409, 416, 444, 446, 461], "ancestr": [53, 409], "ancom_df": 264, "anderson": [307, 308], "ani": [1, 10, 19, 20, 22, 23, 29, 31, 41, 42, 45, 80, 81, 114, 116, 118, 119, 123, 124, 128, 129, 130, 141, 145, 148, 152, 154, 158, 159, 167, 179, 181, 184, 189, 220, 226, 233, 252, 259, 264, 266, 269, 306, 309, 313, 318, 322, 333, 338, 344, 346, 347, 361, 366, 390, 400, 402, 408, 411, 414, 416, 417, 423, 427, 435, 436, 437, 439, 440, 455, 468, 470, 480, 492, 493, 495, 502, 504], "anim": 54, "ann": [52, 74], "anndata": 398, "annot": [113, 116, 117, 123, 154], "announc": 123, "anosim": [1, 307, 308], "anoth": [1, 20, 21, 29, 53, 85, 86, 116, 118, 119, 152, 154, 158, 161, 165, 179, 196, 233, 236, 245, 247, 252, 283, 312, 353, 411, 426], "anova": [264, 307, 315, 319], "answer": 491, "anti": [1, 304], "antibiot": [276, 346], "anticip": 504, "anyon": 123, "anyth": [1, 114, 115, 122, 126, 233, 400, 492, 493, 495, 504], "anytim": 123, "anywher": [118, 119, 123, 264], "apart": 460, "api": [114, 179, 258], "app": 122, "appear": [1, 44, 109, 121, 123, 124, 286, 305, 333, 334, 339, 344, 350, 475, 483], "append": [0, 24, 121, 126, 233, 427, 439], "appl": [85, 86], "appli": [0, 1, 19, 20, 23, 83, 86, 87, 88, 91, 113, 114, 119, 123, 125, 154, 165, 174, 175, 177, 178, 189, 220, 226, 233, 252, 261, 287, 299, 300, 306, 309, 313, 333, 347, 360, 381, 387, 390, 396, 403, 411, 416, 421, 427, 439, 481, 492, 504], "applic": [19, 23, 35, 41, 179, 327, 416, 462, 504], "approach": [269, 306, 347, 421, 424], "appropri": [1, 107, 118, 148, 234, 264, 497, 502], "approx": 344, "approxim": [341, 344], "aqfvdhwkel": 112, "aquat": 334, "ar": [0, 1, 3, 19, 20, 22, 23, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 47, 48, 49, 53, 54, 60, 61, 62, 71, 83, 85, 86, 87, 88, 90, 91, 96, 97, 99, 100, 103, 104, 105, 106, 107, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 128, 129, 130, 133, 140, 143, 144, 148, 152, 154, 156, 158, 160, 161, 162, 165, 167, 168, 179, 180, 181, 183, 184, 185, 186, 188, 189, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 204, 207, 208, 209, 210, 215, 220, 222, 223, 225, 226, 228, 229, 230, 231, 232, 233, 234, 238, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 259, 260, 261, 262, 264, 266, 269, 270, 271, 273, 274, 276, 277, 278, 279, 282, 283, 287, 290, 291, 295, 296, 297, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 312, 315, 318, 325, 326, 327, 328, 329, 330, 332, 333, 334, 337, 338, 339, 341, 342, 344, 346, 347, 348, 350, 356, 357, 360, 362, 366, 372, 381, 383, 391, 393, 394, 395, 396, 398, 399, 400, 405, 406, 407, 408, 413, 414, 416, 418, 420, 421, 423, 433, 436, 439, 441, 447, 448, 449, 455, 456, 457, 459, 460, 461, 462, 463, 464, 468, 469, 470, 471, 472, 475, 476, 478, 480, 482, 483, 485, 486, 488, 489, 492, 494, 495, 497, 499, 502, 503, 504], "arang": [372, 377], "arbitrari": [20, 22, 25, 118, 123, 124, 189, 220, 226, 233, 326, 366, 400, 492, 499], "arbitrarili": [480, 504], "archaea": [433, 434, 471], "archiv": [125, 491], "area": [1, 55], "arg": [126, 133, 143, 193, 194, 220, 230, 231, 350], "arginin": 220, "argument": [19, 20, 30, 31, 34, 41, 96, 97, 99, 100, 118, 128, 129, 130, 133, 140, 141, 142, 143, 144, 145, 146, 160, 162, 186, 188, 191, 193, 194, 195, 223, 225, 228, 230, 231, 232, 243, 248, 251, 252, 262, 287, 290, 296, 299, 301, 303, 310, 330, 332, 350, 391, 406, 416, 492, 495], "argumentoverridewarn": [140, 144], "aris": [470, 480], "arithmet": 483, "around": [61, 62, 88, 114, 121, 124, 252, 265, 306, 345, 502], "arrai": [1, 3, 4, 5, 6, 8, 9, 10, 15, 17, 19, 23, 27, 53, 71, 85, 86, 94, 95, 98, 102, 105, 114, 120, 189, 201, 203, 206, 211, 215, 219, 220, 224, 226, 233, 245, 247, 250, 252, 254, 256, 262, 263, 265, 266, 267, 268, 270, 271, 272, 273, 275, 276, 277, 278, 279, 280, 282, 283, 291, 298, 312, 313, 318, 322, 325, 327, 338, 342, 344, 345, 346, 347, 348, 349, 353, 354, 355, 356, 357, 359, 360, 373, 376, 380, 384, 386, 390, 392, 396, 397, 400, 403, 416, 438, 470, 480, 499], "arrang": 327, "array_lik": [1, 3, 4, 5, 6, 14, 15, 16, 20, 44, 45, 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notranslate\"><span class=\"pre\">skbio.io.format.biom</span></code>)", "BLAST+6 format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.blast6</span></code>)", "BLAST+7 format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.blast7</span></code>)", "Clustal format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.clustal</span></code>)", "Embedding format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.embed</span></code>).", "EMBL format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.embl</span></code>)", "FASTA/QUAL format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.fasta</span></code>)", "FASTQ format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.fastq</span></code>)", "GenBank format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.genbank</span></code>)", "GFF3 format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.gff3</span></code>)", "Labeled square matrix format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.lsmat</span></code>)", "Newick format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.newick</span></code>)", "Ordination results format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.ordination</span></code>)", "PHYLIP multiple sequence alignment format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.phylip</span></code>)", "QSeq format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.qseq</span></code>)", "Format Support", "Stockholm format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.stockholm</span></code>)", "Taxdump format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.taxdump</span></code>)", "I/O Registry (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.registry</span></code>)", "skbio.io.registry.Format", "skbio.io.registry.Format.reader", "skbio.io.registry.Format.sniffer", "skbio.io.registry.Format.writer", "skbio.io.registry.IORegistry", "skbio.io.registry.IORegistry.add_format", "skbio.io.registry.IORegistry.create_format", "skbio.io.registry.IORegistry.get_reader", "skbio.io.registry.IORegistry.get_sniffer", "skbio.io.registry.IORegistry.get_writer", "skbio.io.registry.IORegistry.list_read_formats", "skbio.io.registry.IORegistry.list_write_formats", "skbio.io.registry.IORegistry.monkey_patch", "skbio.io.registry.IORegistry.read", "skbio.io.registry.IORegistry.sniff", "skbio.io.registry.IORegistry.write", "skbio.io.registry.create_format", "skbio.io.registry.read", "skbio.io.registry.sniff", "skbio.io.registry.write", "I/O utilities (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.util</span></code>)", "skbio.io.util.open", "skbio.io.util.open_file", "skbio.io.util.open_files", "skbio.metadata.CategoricalMetadataColumn", "skbio.metadata.Interval", "skbio.metadata.Interval.drop", "skbio.metadata.IntervalMetadata", "skbio.metadata.IntervalMetadata.add", "skbio.metadata.IntervalMetadata.concat", "skbio.metadata.IntervalMetadata.drop", "skbio.metadata.IntervalMetadata.merge", "skbio.metadata.IntervalMetadata.query", "skbio.metadata.IntervalMetadata.read", "skbio.metadata.IntervalMetadata.sort", "skbio.metadata.IntervalMetadata.write", "skbio.metadata.IntervalMetadataMixin", "skbio.metadata.IntervalMetadataMixin.has_interval_metadata", "skbio.metadata.MetadataColumn", "skbio.metadata.MetadataColumn.drop_missing_values", "skbio.metadata.MetadataColumn.filter_ids", "skbio.metadata.MetadataColumn.get_ids", "skbio.metadata.MetadataColumn.get_missing", "skbio.metadata.MetadataColumn.get_value", "skbio.metadata.MetadataColumn.has_missing_values", "skbio.metadata.MetadataColumn.to_dataframe", "skbio.metadata.MetadataColumn.to_series", "skbio.metadata.MetadataMixin", "skbio.metadata.MetadataMixin.has_metadata", "skbio.metadata.NumericMetadataColumn", "skbio.metadata.PositionalMetadataMixin", "skbio.metadata.PositionalMetadataMixin.has_positional_metadata", "skbio.metadata.SampleMetadata", "skbio.metadata.SampleMetadata.filter_columns", "skbio.metadata.SampleMetadata.filter_ids", "skbio.metadata.SampleMetadata.get_column", "skbio.metadata.SampleMetadata.get_ids", "skbio.metadata.SampleMetadata.load", "skbio.metadata.SampleMetadata.merge", "skbio.metadata.SampleMetadata.read", "skbio.metadata.SampleMetadata.to_dataframe", "skbio.metadata.SampleMetadata.write", "skbio.sequence.DNA", "skbio.sequence.DNA.find_motifs", "skbio.sequence.DNA.read", "skbio.sequence.DNA.transcribe", "skbio.sequence.DNA.translate", "skbio.sequence.DNA.translate_six_frames", "skbio.sequence.DNA.write", "skbio.sequence.GeneticCode", "skbio.sequence.GeneticCode.from_ncbi", "skbio.sequence.GeneticCode.translate", "skbio.sequence.GeneticCode.translate_six_frames", "skbio.sequence.GrammaredSequence", "skbio.sequence.GrammaredSequence.definites", "skbio.sequence.GrammaredSequence.degap", "skbio.sequence.GrammaredSequence.degenerates", "skbio.sequence.GrammaredSequence.expand_degenerates", "skbio.sequence.GrammaredSequence.find_motifs", "skbio.sequence.GrammaredSequence.gaps", "skbio.sequence.GrammaredSequence.has_definites", "skbio.sequence.GrammaredSequence.has_degenerates", "skbio.sequence.GrammaredSequence.has_gaps", "skbio.sequence.GrammaredSequence.has_nondegenerates", "skbio.sequence.GrammaredSequence.nondegenerates", "skbio.sequence.GrammaredSequence.to_definites", "skbio.sequence.GrammaredSequence.to_regex", "skbio.sequence.NucleotideMixin", "skbio.sequence.NucleotideMixin.complement", "skbio.sequence.NucleotideMixin.gc_content", "skbio.sequence.NucleotideMixin.gc_frequency", "skbio.sequence.NucleotideMixin.is_reverse_complement", "skbio.sequence.NucleotideMixin.reverse_complement", "skbio.sequence.Protein", "skbio.sequence.Protein.find_motifs", "skbio.sequence.Protein.has_stops", "skbio.sequence.Protein.read", "skbio.sequence.Protein.stops", "skbio.sequence.Protein.write", "skbio.sequence.RNA", "skbio.sequence.RNA.find_motifs", "skbio.sequence.RNA.read", "skbio.sequence.RNA.reverse_transcribe", "skbio.sequence.RNA.translate", "skbio.sequence.RNA.translate_six_frames", "skbio.sequence.RNA.write", "skbio.sequence.Sequence", "skbio.sequence.Sequence.concat", "skbio.sequence.Sequence.count", "skbio.sequence.Sequence.distance", "skbio.sequence.Sequence.find_with_regex", "skbio.sequence.Sequence.frequencies", "skbio.sequence.Sequence.index", "skbio.sequence.Sequence.iter_contiguous", "skbio.sequence.Sequence.iter_kmers", "skbio.sequence.Sequence.kmer_frequencies", "skbio.sequence.Sequence.lowercase", "skbio.sequence.Sequence.match_frequency", "skbio.sequence.Sequence.matches", "skbio.sequence.Sequence.mismatch_frequency", "skbio.sequence.Sequence.mismatches", "skbio.sequence.Sequence.read", "skbio.sequence.Sequence.replace", "skbio.sequence.Sequence.to_indices", "skbio.sequence.Sequence.write", "skbio.sequence.SubstitutionMatrix", "skbio.sequence.SubstitutionMatrix.by_name", "skbio.sequence.SubstitutionMatrix.from_dict", "skbio.sequence.SubstitutionMatrix.get_names", "skbio.sequence.SubstitutionMatrix.identity", "skbio.sequence.SubstitutionMatrix.to_dict", "Sequence distance metrics (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.sequence.distance</span></code>)", "skbio.sequence.distance.hamming", "skbio.sequence.distance.kmer_distance", "Composition Statistics (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.stats.composition</span></code>)", "skbio.stats.composition.alr", "skbio.stats.composition.alr_inv", "skbio.stats.composition.ancom", "skbio.stats.composition.centralize", "skbio.stats.composition.closure", "skbio.stats.composition.clr", "skbio.stats.composition.clr_inv", "skbio.stats.composition.dirmult_ttest", "skbio.stats.composition.ilr", "skbio.stats.composition.ilr_inv", "skbio.stats.composition.inner", "skbio.stats.composition.multi_replace", "skbio.stats.composition.multiplicative_replacement", "skbio.stats.composition.pairwise_vlr", "skbio.stats.composition.perturb", "skbio.stats.composition.perturb_inv", "skbio.stats.composition.power", "skbio.stats.composition.sbp_basis", "skbio.stats.composition.tree_basis", "skbio.stats.composition.vlr", "Distance matrix-based statistics (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.stats.distance</span></code>)", "skbio.stats.distance.DissimilarityMatrix", "skbio.stats.distance.DissimilarityMatrix.between", "skbio.stats.distance.DissimilarityMatrix.copy", "skbio.stats.distance.DissimilarityMatrix.filter", "skbio.stats.distance.DissimilarityMatrix.from_iterable", "skbio.stats.distance.DissimilarityMatrix.index", "skbio.stats.distance.DissimilarityMatrix.plot", "skbio.stats.distance.DissimilarityMatrix.read", "skbio.stats.distance.DissimilarityMatrix.redundant_form", "skbio.stats.distance.DissimilarityMatrix.rename", "skbio.stats.distance.DissimilarityMatrix.to_data_frame", "skbio.stats.distance.DissimilarityMatrix.transpose", "skbio.stats.distance.DissimilarityMatrix.within", "skbio.stats.distance.DissimilarityMatrix.write", "skbio.stats.distance.DistanceMatrix", "skbio.stats.distance.DistanceMatrix.condensed_form", "skbio.stats.distance.DistanceMatrix.from_iterable", "skbio.stats.distance.DistanceMatrix.permute", "skbio.stats.distance.DistanceMatrix.read", "skbio.stats.distance.DistanceMatrix.to_series", "skbio.stats.distance.DistanceMatrix.write", "skbio.stats.distance.anosim", "skbio.stats.distance.bioenv", "skbio.stats.distance.mantel", "skbio.stats.distance.permanova", "skbio.stats.distance.permdisp", "skbio.stats.distance.pwmantel", "skbio.stats.distance.randdm", "Evolutionary statistics (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.stats.evolve</span></code>)", "skbio.stats.evolve.hommola_cospeciation", "Gradient analyses (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.stats.gradient</span></code>)", "skbio.stats.gradient.AverageGradientANOVA", "skbio.stats.gradient.CategoryResults", "skbio.stats.gradient.CategoryResults.to_files", "skbio.stats.gradient.FirstDifferenceGradientANOVA", "skbio.stats.gradient.GradientANOVA", "skbio.stats.gradient.GradientANOVA.get_trajectories", "skbio.stats.gradient.GradientANOVAResults", "skbio.stats.gradient.GradientANOVAResults.to_files", "skbio.stats.gradient.GroupResults", "skbio.stats.gradient.GroupResults.to_files", "skbio.stats.gradient.TrajectoryGradientANOVA", "skbio.stats.gradient.WindowDifferenceGradientANOVA", "skbio.stats.isubsample", "Ordination methods (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.stats.ordination</span></code>)", "skbio.stats.ordination.OrdinationResults", "skbio.stats.ordination.OrdinationResults.plot", "skbio.stats.ordination.OrdinationResults.read", "skbio.stats.ordination.OrdinationResults.rename", "skbio.stats.ordination.OrdinationResults.write", "skbio.stats.ordination.ca", "skbio.stats.ordination.cca", "skbio.stats.ordination.corr", "skbio.stats.ordination.e_matrix", "skbio.stats.ordination.f_matrix", "skbio.stats.ordination.mean_and_std", "skbio.stats.ordination.pcoa", "skbio.stats.ordination.pcoa_biplot", "skbio.stats.ordination.rda", "skbio.stats.ordination.scale", "skbio.stats.ordination.svd_rank", "Empirical Power Estimation (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.stats.power</span></code>)", "skbio.stats.power.confidence_bound", "skbio.stats.power.paired_subsamples", "skbio.stats.power.subsample_paired_power", "skbio.stats.power.subsample_power", "skbio.stats.subsample_counts", "skbio.table.Table", "skbio.table.Table.add_group_metadata", "skbio.table.Table.add_metadata", "skbio.table.Table.align_to", "skbio.table.Table.align_to_dataframe", "skbio.table.Table.align_tree", "skbio.table.Table.collapse", "skbio.table.Table.concat", "skbio.table.Table.copy", "skbio.table.Table.data", "skbio.table.Table.del_metadata", "skbio.table.Table.delimited_self", "skbio.table.Table.descriptive_equality", "skbio.table.Table.exists", "skbio.table.Table.filter", "skbio.table.Table.from_adjacency", "skbio.table.Table.from_hdf5", "skbio.table.Table.from_json", "skbio.table.Table.from_tsv", "skbio.table.Table.get_table_density", "skbio.table.Table.get_value_by_ids", "skbio.table.Table.group_metadata", "skbio.table.Table.head", "skbio.table.Table.ids", "skbio.table.Table.index", "skbio.table.Table.is_empty", "skbio.table.Table.iter", "skbio.table.Table.iter_data", "skbio.table.Table.iter_pairwise", "skbio.table.Table.length", "skbio.table.Table.max", "skbio.table.Table.merge", "skbio.table.Table.metadata", "skbio.table.Table.metadata_to_dataframe", "skbio.table.Table.min", "skbio.table.Table.nonzero", "skbio.table.Table.nonzero_counts", "skbio.table.Table.norm", "skbio.table.Table.pa", "skbio.table.Table.partition", "skbio.table.Table.rankdata", "skbio.table.Table.read", "skbio.table.Table.reduce", "skbio.table.Table.remove_empty", "skbio.table.Table.sort", "skbio.table.Table.sort_order", "skbio.table.Table.subsample", "skbio.table.Table.sum", "skbio.table.Table.to_anndata", "skbio.table.Table.to_dataframe", "skbio.table.Table.to_hdf5", "skbio.table.Table.to_json", "skbio.table.Table.to_tsv", "skbio.table.Table.transform", "skbio.table.Table.transpose", "skbio.table.Table.update_ids", "skbio.table.Table.write", "skbio.table.example_table", "skbio.tree.TreeNode", "skbio.tree.TreeNode.accumulate_to_ancestor", "skbio.tree.TreeNode.ancestors", "skbio.tree.TreeNode.append", "skbio.tree.TreeNode.ascii_art", "skbio.tree.TreeNode.assign_ids", "skbio.tree.TreeNode.assign_supports", "skbio.tree.TreeNode.bifurcate", "skbio.tree.TreeNode.cache_attr", "skbio.tree.TreeNode.clear_caches", "skbio.tree.TreeNode.compare_rfd", "skbio.tree.TreeNode.compare_subsets", "skbio.tree.TreeNode.compare_tip_distances", "skbio.tree.TreeNode.copy", "skbio.tree.TreeNode.count", "skbio.tree.TreeNode.create_caches", "skbio.tree.TreeNode.deepcopy", "skbio.tree.TreeNode.descending_branch_length", "skbio.tree.TreeNode.distance", "skbio.tree.TreeNode.extend", "skbio.tree.TreeNode.find", "skbio.tree.TreeNode.find_all", "skbio.tree.TreeNode.find_by_func", "skbio.tree.TreeNode.find_by_id", "skbio.tree.TreeNode.from_linkage_matrix", "skbio.tree.TreeNode.from_taxdump", "skbio.tree.TreeNode.from_taxonomy", "skbio.tree.TreeNode.get_max_distance", "skbio.tree.TreeNode.has_caches", "skbio.tree.TreeNode.has_children", "skbio.tree.TreeNode.index_tree", "skbio.tree.TreeNode.insert", "skbio.tree.TreeNode.invalidate_caches", "skbio.tree.TreeNode.is_bifurcating", "skbio.tree.TreeNode.is_root", "skbio.tree.TreeNode.is_tip", "skbio.tree.TreeNode.lca", "skbio.tree.TreeNode.levelorder", "skbio.tree.TreeNode.lowest_common_ancestor", "skbio.tree.TreeNode.neighbors", "skbio.tree.TreeNode.non_tips", "skbio.tree.TreeNode.observed_node_counts", "skbio.tree.TreeNode.pop", "skbio.tree.TreeNode.postorder", "skbio.tree.TreeNode.pre_and_postorder", "skbio.tree.TreeNode.preorder", "skbio.tree.TreeNode.prune", "skbio.tree.TreeNode.remove", "skbio.tree.TreeNode.remove_by_func", "skbio.tree.TreeNode.remove_deleted", "skbio.tree.TreeNode.root", "skbio.tree.TreeNode.root_at", "skbio.tree.TreeNode.root_at_midpoint", "skbio.tree.TreeNode.root_by_outgroup", "skbio.tree.TreeNode.shear", "skbio.tree.TreeNode.shuffle", "skbio.tree.TreeNode.siblings", "skbio.tree.TreeNode.subset", "skbio.tree.TreeNode.subsets", "skbio.tree.TreeNode.subtree", "skbio.tree.TreeNode.tip_tip_distances", "skbio.tree.TreeNode.tips", "skbio.tree.TreeNode.to_array", "skbio.tree.TreeNode.to_taxonomy", "skbio.tree.TreeNode.traverse", "skbio.tree.TreeNode.unpack", "skbio.tree.TreeNode.unpack_by_func", "skbio.tree.TreeNode.unroot", "skbio.tree.TreeNode.unrooted_copy", "skbio.tree.TreeNode.unrooted_deepcopy", "skbio.tree.TreeNode.unrooted_move", "skbio.tree.gme", "skbio.tree.majority_rule", "skbio.tree.nj", "skbio.tree.nni", "skbio.tree.upgma", "skbio.util.PlottableMixin", "skbio.util.assert_data_frame_almost_equal", "skbio.util.assert_ordination_results_equal", "skbio.util.cardinal_to_ordinal", "skbio.util.classproperty", "skbio.util.find_duplicates", "skbio.util.get_data_path", "skbio.util.safe_md5", "skbio.workflow.Workflow", "skbio.workflow.Workflow.initialize_state", "skbio.workflow.method", "skbio.workflow.requires", "Home", "Input and Output (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io</span></code>)", "Metadata (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.metadata</span></code>)", "Biological Sequences (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.sequence</span></code>)", "Multivariate Statistics (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.stats</span></code>)", "Data Table (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.table</span></code>)", "Trees and Phylogenetics (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.tree</span></code>)", "Utilities for Developers (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.util</span></code>)", "Workflow construction (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.workflow</span></code>)"], "titleterms": {"0": 496, "3": 496, "6": [109, 496], "7": 110, "abstract": [498, 499], "ac": 44, "accumulate_to_ancestor": 409, "ad": 119, "add": 155, "add_format": 132, "add_group_metadata": 351, "add_metadata": 352, "advanc": 119, "algorithm": 0, "align": [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 111, 121, 124], "align_to": 353, "align_to_datafram": 354, "align_tre": 355, "alignmentstructur": [11, 12, 13], "alignpath": [3, 4, 5, 6, 7, 8, 9, 10], "alpha": [1, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82], "alpha_divers": 83, "alr": 262, "alr_inv": 263, "analys": 313, "analysi": 327, "ancestor": 410, "ancom": 264, "anosim": 304, "append": [21, 411], "applic": 119, "argument": 126, "ascii_art": 412, "assert_data_frame_almost_equ": 485, "assert_ordination_results_equ": 486, "assign_id": 413, "assign_support": 414, "averagegradientanova": 314, "base": 282, "basic": 119, "befor": [113, 116], "berger_parker_d": 45, "beta": [1, 84, 85, 86], "beta_divers": 87, "between": 284, "bifurc": 415, "binari": 107, "binary_dm": 107, "bio": [126, 496, 497], "bioenv": 305, "biolog": [2, 499], "biom": [108, 501], "blast": [109, 110], "blast6": 109, "blast7": 110, "block_beta_divers": 88, "brillouin_d": 46, "by_nam": 253, "byte": 93, "ca": 333, "cache_attr": 416, "calcul": 499, "can": 497, "canon": 327, "cardinal_to_ordin": 487, "categor": 282, "categoricalmetadatacolumn": 151, "categoryresult": [315, 316], "caveat": 119, "cca": 334, "central": 265, "chao1": 47, "chao1_ci": 48, "charact": 123, "class": [126, 282, 313, 498, 499, 504], "classproperti": 488, "clear_cach": 417, "closur": 266, "clr": 267, "clr_inv": 268, "clustal": 111, "collaps": 356, "column": [109, 110, 123, 498], "comment": [119, 123], "commun": 1, "compare_rfd": 418, "compare_subset": 419, "compare_tip_dist": 420, "comparison": 282, "complement": 215, "composit": [261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 500], "concat": [156, 234, 357], "condensed_form": 298, "confidence_bound": 345, "consensu": 22, "conserv": 23, "construct": 504, "continu": 282, "cophylogenet": 311, "copi": [285, 358, 421], "corr": 335, "correspond": 327, "count": [1, 235, 422], "coverag": 43, "creat": 126, "create_cach": 423, "create_format": [133, 143], "custom": 497, "data": [0, 114, 282, 359, 500, 501], "decor": 504, "deepcopi": 424, "definit": 201, "degap": 202, "degener": 203, "del_metadata": 360, 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