From d169b3e0c41ea0c11e89ca56390c8691e2f4f8c1 Mon Sep 17 00:00:00 2001
From: qiyunzhu <4396343+qiyunzhu@users.noreply.github.com>
Date: Tue, 26 Mar 2024 22:54:24 +0000
Subject: [PATCH] Update from
 https://github.com/scikit-bio/scikit-bio/commit/a2ca94a93c269295ff5e8594aa78e7d7ec303e1c

---
 .../generated/skbio.io.format.biom.rst.txt    |  19 +
 .../skbio.io.ArgumentOverrideWarning.html     |   1 +
 .../generated/skbio.io.BLAST7FormatError.html |   1 +
 .../skbio.io.ClustalFormatError.html          |   1 +
 .../generated/skbio.io.EMBLFormatError.html   |   1 +
 .../generated/skbio.io.FASTAFormatError.html  |   1 +
 .../generated/skbio.io.FASTQFormatError.html  |   1 +
 .../generated/skbio.io.FileFormatError.html   |   1 +
 .../skbio.io.FormatIdentificationWarning.html |   1 +
 .../generated/skbio.io.GFF3FormatError.html   |   1 +
 .../skbio.io.GenBankFormatError.html          |   1 +
 .../dev/generated/skbio.io.IOSourceError.html |   1 +
 .../generated/skbio.io.LSMatFormatError.html  |   1 +
 .../generated/skbio.io.NewickFormatError.html |   1 +
 .../skbio.io.OrdinationFormatError.html       |   1 +
 .../generated/skbio.io.PhylipFormatError.html |   1 +
 .../generated/skbio.io.QSeqFormatError.html   |   1 +
 .../generated/skbio.io.QUALFormatError.html   |   1 +
 .../skbio.io.StockholmFormatError.html        |   1 +
 .../skbio.io.UnrecognizedFormatError.html     |   1 +
 .../generated/skbio.io.format.binary_dm.html  |   7 +-
 docs/dev/generated/skbio.io.format.biom.html  | 884 ++++++++++++++++++
 .../dev/generated/skbio.io.format.blast6.html |   7 +-
 .../dev/generated/skbio.io.format.blast7.html |   1 +
 .../generated/skbio.io.format.clustal.html    |   1 +
 docs/dev/generated/skbio.io.format.embl.html  |   1 +
 docs/dev/generated/skbio.io.format.fasta.html |   1 +
 docs/dev/generated/skbio.io.format.fastq.html |   1 +
 .../generated/skbio.io.format.genbank.html    |   1 +
 docs/dev/generated/skbio.io.format.gff3.html  |   1 +
 docs/dev/generated/skbio.io.format.lsmat.html |   1 +
 .../dev/generated/skbio.io.format.newick.html |   1 +
 .../generated/skbio.io.format.ordination.html |   1 +
 .../dev/generated/skbio.io.format.phylip.html |   1 +
 docs/dev/generated/skbio.io.format.qseq.html  |   1 +
 .../skbio.io.format.sample_metadata.html      |   1 +
 .../generated/skbio.io.format.stockholm.html  |   1 +
 .../generated/skbio.io.format.taxdump.html    |   1 +
 ...o.registry.DuplicateRegistrationError.html |   1 +
 .../skbio.io.registry.Format.__eq__.html      |   1 +
 .../skbio.io.registry.Format.__ge__.html      |   1 +
 ...skbio.io.registry.Format.__getstate__.html |   1 +
 .../skbio.io.registry.Format.__gt__.html      |   1 +
 .../skbio.io.registry.Format.__hash__.html    |   1 +
 .../skbio.io.registry.Format.__le__.html      |   1 +
 .../skbio.io.registry.Format.__lt__.html      |   1 +
 .../skbio.io.registry.Format.__ne__.html      |   1 +
 .../skbio.io.registry.Format.__str__.html     |   1 +
 .../generated/skbio.io.registry.Format.html   |   1 +
 .../skbio.io.registry.Format.reader.html      |   1 +
 .../skbio.io.registry.Format.sniffer.html     |   1 +
 .../skbio.io.registry.Format.writer.html      |   1 +
 .../skbio.io.registry.IORegistry.__eq__.html  |   1 +
 .../skbio.io.registry.IORegistry.__ge__.html  |   1 +
 ...o.io.registry.IORegistry.__getstate__.html |   1 +
 .../skbio.io.registry.IORegistry.__gt__.html  |   1 +
 ...skbio.io.registry.IORegistry.__hash__.html |   1 +
 .../skbio.io.registry.IORegistry.__le__.html  |   1 +
 .../skbio.io.registry.IORegistry.__lt__.html  |   1 +
 .../skbio.io.registry.IORegistry.__ne__.html  |   1 +
 .../skbio.io.registry.IORegistry.__str__.html |   1 +
 ...bio.io.registry.IORegistry.add_format.html |   1 +
 ....io.registry.IORegistry.create_format.html |   1 +
 ...bio.io.registry.IORegistry.get_reader.html |   1 +
 ...io.io.registry.IORegistry.get_sniffer.html |   1 +
 ...bio.io.registry.IORegistry.get_writer.html |   1 +
 .../skbio.io.registry.IORegistry.html         |   1 +
 ...registry.IORegistry.list_read_formats.html |   1 +
 ...egistry.IORegistry.list_write_formats.html |   1 +
 ...o.io.registry.IORegistry.monkey_patch.html |   1 +
 .../skbio.io.registry.IORegistry.read.html    |   1 +
 .../skbio.io.registry.IORegistry.sniff.html   |   1 +
 .../skbio.io.registry.IORegistry.write.html   |   1 +
 ....io.registry.InvalidRegistrationError.html |   1 +
 .../skbio.io.registry.create_format.html      |   1 +
 docs/dev/generated/skbio.io.registry.html     |   1 +
 .../dev/generated/skbio.io.registry.read.html |   1 +
 .../generated/skbio.io.registry.sniff.html    |   1 +
 .../generated/skbio.io.registry.write.html    |   1 +
 docs/dev/generated/skbio.io.util.html         |   1 +
 docs/dev/generated/skbio.io.util.open.html    |   1 +
 .../generated/skbio.io.util.open_file.html    |   1 +
 .../generated/skbio.io.util.open_files.html   |   1 +
 docs/dev/genindex.html                        |  13 +-
 docs/dev/io.html                              |  36 +-
 docs/dev/objects.inv                          | Bin 21388 -> 21426 bytes
 docs/dev/py-modindex.html                     |   5 +
 docs/dev/searchindex.js                       |   2 +-
 88 files changed, 1027 insertions(+), 25 deletions(-)
 create mode 100644 docs/dev/_sources/generated/skbio.io.format.biom.rst.txt
 create mode 100644 docs/dev/generated/skbio.io.format.biom.html

diff --git a/docs/dev/_sources/generated/skbio.io.format.biom.rst.txt b/docs/dev/_sources/generated/skbio.io.format.biom.rst.txt
new file mode 100644
index 000000000..17a92727b
--- /dev/null
+++ b/docs/dev/_sources/generated/skbio.io.format.biom.rst.txt
@@ -0,0 +1,19 @@
+..
+  The extra blocks seem to be required for autosummary to populate our
+  docstrings correctly. In the original template, these would recusively call
+  autosummary again, but we already do that in the narratively convenient
+  places.
+
+.. automodule:: skbio.io.format.biom
+
+   
+   
+
+   
+   
+
+   
+   
+
+   
+   
\ No newline at end of file
diff --git a/docs/dev/generated/skbio.io.ArgumentOverrideWarning.html b/docs/dev/generated/skbio.io.ArgumentOverrideWarning.html
index d3414b12c..6fceccf50 100644
--- a/docs/dev/generated/skbio.io.ArgumentOverrideWarning.html
+++ b/docs/dev/generated/skbio.io.ArgumentOverrideWarning.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.BLAST7FormatError.html b/docs/dev/generated/skbio.io.BLAST7FormatError.html
index 36200ad60..f2f67ea41 100644
--- a/docs/dev/generated/skbio.io.BLAST7FormatError.html
+++ b/docs/dev/generated/skbio.io.BLAST7FormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.ClustalFormatError.html b/docs/dev/generated/skbio.io.ClustalFormatError.html
index 6c1a86b4b..13e312623 100644
--- a/docs/dev/generated/skbio.io.ClustalFormatError.html
+++ b/docs/dev/generated/skbio.io.ClustalFormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.EMBLFormatError.html b/docs/dev/generated/skbio.io.EMBLFormatError.html
index 504a1dec2..cb82781c3 100644
--- a/docs/dev/generated/skbio.io.EMBLFormatError.html
+++ b/docs/dev/generated/skbio.io.EMBLFormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.FASTAFormatError.html b/docs/dev/generated/skbio.io.FASTAFormatError.html
index e7e167a49..67d569ec2 100644
--- a/docs/dev/generated/skbio.io.FASTAFormatError.html
+++ b/docs/dev/generated/skbio.io.FASTAFormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.FASTQFormatError.html b/docs/dev/generated/skbio.io.FASTQFormatError.html
index a447cf252..5499b48e7 100644
--- a/docs/dev/generated/skbio.io.FASTQFormatError.html
+++ b/docs/dev/generated/skbio.io.FASTQFormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.FileFormatError.html b/docs/dev/generated/skbio.io.FileFormatError.html
index fab1a4657..5bd7768a8 100644
--- a/docs/dev/generated/skbio.io.FileFormatError.html
+++ b/docs/dev/generated/skbio.io.FileFormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.FormatIdentificationWarning.html b/docs/dev/generated/skbio.io.FormatIdentificationWarning.html
index 983d44cfa..a02180f12 100644
--- a/docs/dev/generated/skbio.io.FormatIdentificationWarning.html
+++ b/docs/dev/generated/skbio.io.FormatIdentificationWarning.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.GFF3FormatError.html b/docs/dev/generated/skbio.io.GFF3FormatError.html
index e962189a8..1669d2f00 100644
--- a/docs/dev/generated/skbio.io.GFF3FormatError.html
+++ b/docs/dev/generated/skbio.io.GFF3FormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.GenBankFormatError.html b/docs/dev/generated/skbio.io.GenBankFormatError.html
index 88f05ca46..40b927719 100644
--- a/docs/dev/generated/skbio.io.GenBankFormatError.html
+++ b/docs/dev/generated/skbio.io.GenBankFormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.IOSourceError.html b/docs/dev/generated/skbio.io.IOSourceError.html
index 3c9223aa9..2c64b36c1 100644
--- a/docs/dev/generated/skbio.io.IOSourceError.html
+++ b/docs/dev/generated/skbio.io.IOSourceError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.LSMatFormatError.html b/docs/dev/generated/skbio.io.LSMatFormatError.html
index 74b413151..0cc7d57fb 100644
--- a/docs/dev/generated/skbio.io.LSMatFormatError.html
+++ b/docs/dev/generated/skbio.io.LSMatFormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.NewickFormatError.html b/docs/dev/generated/skbio.io.NewickFormatError.html
index 7529bbcd1..0afefda59 100644
--- a/docs/dev/generated/skbio.io.NewickFormatError.html
+++ b/docs/dev/generated/skbio.io.NewickFormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.OrdinationFormatError.html b/docs/dev/generated/skbio.io.OrdinationFormatError.html
index 73dcb87cf..d4a963b8b 100644
--- a/docs/dev/generated/skbio.io.OrdinationFormatError.html
+++ b/docs/dev/generated/skbio.io.OrdinationFormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.PhylipFormatError.html b/docs/dev/generated/skbio.io.PhylipFormatError.html
index ff18508d3..6f637a140 100644
--- a/docs/dev/generated/skbio.io.PhylipFormatError.html
+++ b/docs/dev/generated/skbio.io.PhylipFormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.QSeqFormatError.html b/docs/dev/generated/skbio.io.QSeqFormatError.html
index 22a6d05ed..22380d43a 100644
--- a/docs/dev/generated/skbio.io.QSeqFormatError.html
+++ b/docs/dev/generated/skbio.io.QSeqFormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.QUALFormatError.html b/docs/dev/generated/skbio.io.QUALFormatError.html
index 3f5dfa16d..c4f23b461 100644
--- a/docs/dev/generated/skbio.io.QUALFormatError.html
+++ b/docs/dev/generated/skbio.io.QUALFormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.StockholmFormatError.html b/docs/dev/generated/skbio.io.StockholmFormatError.html
index b4f9df246..6f842906e 100644
--- a/docs/dev/generated/skbio.io.StockholmFormatError.html
+++ b/docs/dev/generated/skbio.io.StockholmFormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.UnrecognizedFormatError.html b/docs/dev/generated/skbio.io.UnrecognizedFormatError.html
index 08ef67453..85ff27626 100644
--- a/docs/dev/generated/skbio.io.UnrecognizedFormatError.html
+++ b/docs/dev/generated/skbio.io.UnrecognizedFormatError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.format.binary_dm.html b/docs/dev/generated/skbio.io.format.binary_dm.html
index 81266a37f..15b1d56a1 100644
--- a/docs/dev/generated/skbio.io.format.binary_dm.html
+++ b/docs/dev/generated/skbio.io.format.binary_dm.html
@@ -69,7 +69,7 @@
     <link rel="icon" href="../_static/favicon.ico"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="BLAST+6 format (skbio.io.format.blast6)" href="skbio.io.format.blast6.html" />
+    <link rel="next" title="BIOM-Format (skbio.io.format.biom)" href="skbio.io.format.biom.html" />
     <link rel="prev" title="File I/O (skbio.io)" href="../io.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
@@ -819,11 +820,11 @@ <h2>References<a class="headerlink" href="#references" title="Link to this headi
       </div>
     </a>
     <a class="right-next"
-       href="skbio.io.format.blast6.html"
+       href="skbio.io.format.biom.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</p>
+        <p class="prev-next-title">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/docs/dev/generated/skbio.io.format.biom.html b/docs/dev/generated/skbio.io.format.biom.html
new file mode 100644
index 000000000..78c45baef
--- /dev/null
+++ b/docs/dev/generated/skbio.io.format.biom.html
@@ -0,0 +1,884 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../" >
+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
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+  
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+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+<link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.1/webfonts/fa-regular-400.woff2" />
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+    <script>
+        DOCUMENTATION_OPTIONS.theme_version = '0.15.2';
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+        DOCUMENTATION_OPTIONS.theme_switcher_version_match = 'dev';
+        DOCUMENTATION_OPTIONS.show_version_warning_banner = false;
+        </script>
+    <link rel="canonical" href="../../../generated/skbio.io.format.biom.html" />
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+  <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1 current active"><a class="current reference internal" href="#">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
+
+
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.clustal.html">Clustal format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.clustal</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.embl.html">EMBL format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.embl</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.fasta.html">FASTA/QUAL format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.fasta</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.fastq.html">FASTQ format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.fastq</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.genbank.html">GenBank format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.genbank</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.gff3.html">GFF3 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.gff3</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.lsmat.html">Labeled square matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.lsmat</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.newick.html">Newick format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.newick</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.ordination.html">Ordination results format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.ordination</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.phylip.html">PHYLIP multiple sequence alignment format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.phylip</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.qseq.html">QSeq format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.qseq</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.stockholm.html">Stockholm format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.stockholm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.taxdump.html">Taxdump format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.taxdump</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.sample_metadata.html">Format Support</a></li>
+
+</ul>
+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.registry.write.html">skbio.io.registry.write</a></li>
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+<li class="toctree-l1"><a class="reference internal" href="skbio.io.registry.sniff.html">skbio.io.registry.sniff</a></li>
+</ul>
+<ul class="nav bd-sidenav">
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+<li class="toctree-l1"><a class="reference internal" href="skbio.io.LSMatFormatError.html">skbio.io.LSMatFormatError</a></li>
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+<li class="toctree-l1"><a class="reference internal" href="skbio.io.QUALFormatError.html">skbio.io.QUALFormatError</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.StockholmFormatError.html">skbio.io.StockholmFormatError</a></li>
+</ul>
+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.registry.html">I/O Registry (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.registry</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.util.html">I/O utils (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.util</span></code>)</a></li>
+</ul>
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+</nav></div>
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+        
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+      
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+                <article class="bd-article">
+                  
+  <section id="biom-format-skbio-io-format-biom">
+<span id="module-skbio.io.format.biom"></span><h1>BIOM-Format (<a class="reference internal" href="#module-skbio.io.format.biom" title="skbio.io.format.biom"><code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code></a>)<a class="headerlink" href="#biom-format-skbio-io-format-biom" title="Link to this heading">#</a></h1>
+<p>The BIOM-Format (format v2.1.0) is an HDF5-based format to represent sample/feature
+counts or relative abundances. It is designed specifically for sparse data.
+Internally, it stores the data in both compressed sparse row, and compressed
+sparse column representation. It additionally has support for representing sample
+and feature metadata.</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>Internally, BIOM describes features as observations, whereas scikit-bio uses the
+term features.</p>
+</div>
+<section id="format-support">
+<h2>Format Support<a class="headerlink" href="#format-support" title="Link to this heading">#</a></h2>
+<p><strong>Has Sniffer: Yes</strong></p>
+<table class="table">
+<thead>
+<tr class="row-odd"><th class="head"><p>Reader</p></th>
+<th class="head"><p>Writer</p></th>
+<th class="head"><p>Object Class</p></th>
+</tr>
+</thead>
+<tbody>
+<tr class="row-even"><td><p>Yes</p></td>
+<td><p>Yes</p></td>
+<td><p><code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.feature_table.Table</span></code></p></td>
+</tr>
+</tbody>
+</table>
+</section>
+<section id="format-specification">
+<h2>Format Specification<a class="headerlink" href="#format-specification" title="Link to this heading">#</a></h2>
+<p>The official format specification for BIOM-Format can be found at <a class="reference internal" href="#redf92f8d116d-1" id="id1">[1]</a>.</p>
+</section>
+<section id="examples">
+<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading">#</a></h2>
+<p>Here we will write an existing BIOM table, and re-read it. Note that the Table
+from <code class="docutils literal notranslate"><span class="pre">biom</span></code> implicitly gets the <code class="docutils literal notranslate"><span class="pre">.write</span></code> method from the IO registry. This
+<code class="docutils literal notranslate"><span class="pre">ByteIO</span></code> object can be a file path in a regular use case.</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">io</span><span class="o">,</span> <span class="nn">skbio</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">f</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">BytesIO</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">skbio</span><span class="o">.</span><span class="n">feature_table</span><span class="o">.</span><span class="n">example_table</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>  
+<span class="go">&lt;_io.BytesIO object at ...&gt;</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">roundtrip</span> <span class="o">=</span> <span class="n">skbio</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">into</span><span class="o">=</span><span class="n">skbio</span><span class="o">.</span><span class="n">Table</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">roundtrip</span>
+<span class="go">2 x 3 &lt;class &#39;biom.table.Table&#39;&gt; with 5 nonzero entries (83% dense)</span>
+</pre></div>
+</div>
+</section>
+<section id="references">
+<h2>References<a class="headerlink" href="#references" title="Link to this heading">#</a></h2>
+<div role="list" class="citation-list">
+<div class="citation" id="redf92f8d116d-1" role="doc-biblioentry">
+<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id1">1</a><span class="fn-bracket">]</span></span>
+<p><a class="reference external" href="http://biom-format.org/documentation/format_versions/biom-2.1.html">http://biom-format.org/documentation/format_versions/biom-2.1.html</a></p>
+</div>
+</div>
+</section>
+</section>
+
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
+<div class="prev-next-area">
+    <a class="left-prev"
+       href="skbio.io.format.binary_dm.html"
+       title="previous page">
+      <i class="fa-solid fa-angle-left"></i>
+      <div class="prev-next-info">
+        <p class="prev-next-subtitle">previous</p>
+        <p class="prev-next-title">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</p>
+      </div>
+    </a>
+    <a class="right-next"
+       href="skbio.io.format.blast6.html"
+       title="next page">
+      <div class="prev-next-info">
+        <p class="prev-next-subtitle">next</p>
+        <p class="prev-next-title">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</p>
+      </div>
+      <i class="fa-solid fa-angle-right"></i>
+    </a>
+</div>
+                </footer>
+              
+            </div>
+            
+            
+              
+                <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+  <div class="sidebar-secondary-item">
+<div
+    id="pst-page-navigation-heading-2"
+    class="page-toc tocsection onthispage">
+    <i class="fa-solid fa-list"></i> On this page
+  </div>
+  <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
+    <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#format-support">Format Support</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#format-specification">Format Specification</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#examples">Examples</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#references">References</a></li>
+</ul>
+  </nav></div>
+
+</div></div>
+              
+            
+          </div>
+          <footer class="bd-footer-content">
+            
+          </footer>
+        
+      </main>
+    </div>
+  </div>
+  
+  <!-- Scripts loaded after <body> so the DOM is not blocked -->
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+
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+<div class="bd-footer__inner bd-page-width">
+  
+    <div class="footer-items__start">
+      
+        <div class="footer-item">
+
+  <p class="copyright">
+    
+      © Copyright 2014-2024, scikit-bio development team.
+      <br/>
+    
+  </p>
+</div>
+      
+    </div>
+  
+  
+    <div class="footer-items__center">
+      
+        <div class="footer-item">
+
+  <p class="sphinx-version">
+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
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+      
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diff --git a/docs/dev/generated/skbio.io.format.blast6.html b/docs/dev/generated/skbio.io.format.blast6.html
index 5f684676f..a3aea4ab0 100644
--- a/docs/dev/generated/skbio.io.format.blast6.html
+++ b/docs/dev/generated/skbio.io.format.blast6.html
@@ -70,7 +70,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="BLAST+7 format (skbio.io.format.blast7)" href="skbio.io.format.blast7.html" />
-    <link rel="prev" title="Simple binary dissimilarity matrix format (skbio.io.format.binary_dm)" href="skbio.io.format.binary_dm.html" />
+    <link rel="prev" title="BIOM-Format (skbio.io.format.biom)" href="skbio.io.format.biom.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
@@ -1069,12 +1070,12 @@ <h2>References<a class="headerlink" href="#references" title="Link to this headi
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="skbio.io.format.binary_dm.html"
+       href="skbio.io.format.biom.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</p>
+        <p class="prev-next-title">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/docs/dev/generated/skbio.io.format.blast7.html b/docs/dev/generated/skbio.io.format.blast7.html
index c0104c568..1c78f2bc1 100644
--- a/docs/dev/generated/skbio.io.format.blast7.html
+++ b/docs/dev/generated/skbio.io.format.blast7.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.format.clustal.html b/docs/dev/generated/skbio.io.format.clustal.html
index 4a2dcf0f2..279ab5d37 100644
--- a/docs/dev/generated/skbio.io.format.clustal.html
+++ b/docs/dev/generated/skbio.io.format.clustal.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.format.embl.html b/docs/dev/generated/skbio.io.format.embl.html
index 2d29ef7ee..4e35c4b61 100644
--- a/docs/dev/generated/skbio.io.format.embl.html
+++ b/docs/dev/generated/skbio.io.format.embl.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.format.fasta.html b/docs/dev/generated/skbio.io.format.fasta.html
index 4a9292589..d9baca545 100644
--- a/docs/dev/generated/skbio.io.format.fasta.html
+++ b/docs/dev/generated/skbio.io.format.fasta.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.format.fastq.html b/docs/dev/generated/skbio.io.format.fastq.html
index 7ed083bb3..9b9b2dd90 100644
--- a/docs/dev/generated/skbio.io.format.fastq.html
+++ b/docs/dev/generated/skbio.io.format.fastq.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.format.genbank.html b/docs/dev/generated/skbio.io.format.genbank.html
index e5be4451e..c48b74a0c 100644
--- a/docs/dev/generated/skbio.io.format.genbank.html
+++ b/docs/dev/generated/skbio.io.format.genbank.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.format.gff3.html b/docs/dev/generated/skbio.io.format.gff3.html
index 70720bf52..2690af4fb 100644
--- a/docs/dev/generated/skbio.io.format.gff3.html
+++ b/docs/dev/generated/skbio.io.format.gff3.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.format.lsmat.html b/docs/dev/generated/skbio.io.format.lsmat.html
index c7ce4a570..25c358452 100644
--- a/docs/dev/generated/skbio.io.format.lsmat.html
+++ b/docs/dev/generated/skbio.io.format.lsmat.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.format.newick.html b/docs/dev/generated/skbio.io.format.newick.html
index 4c0aadb7f..90a31329b 100644
--- a/docs/dev/generated/skbio.io.format.newick.html
+++ b/docs/dev/generated/skbio.io.format.newick.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.format.ordination.html b/docs/dev/generated/skbio.io.format.ordination.html
index 1c3fe724e..b0cc2186e 100644
--- a/docs/dev/generated/skbio.io.format.ordination.html
+++ b/docs/dev/generated/skbio.io.format.ordination.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.format.phylip.html b/docs/dev/generated/skbio.io.format.phylip.html
index 158ea1414..38e373bb0 100644
--- a/docs/dev/generated/skbio.io.format.phylip.html
+++ b/docs/dev/generated/skbio.io.format.phylip.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.format.qseq.html b/docs/dev/generated/skbio.io.format.qseq.html
index 6cf8ccf60..034fdba96 100644
--- a/docs/dev/generated/skbio.io.format.qseq.html
+++ b/docs/dev/generated/skbio.io.format.qseq.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.format.sample_metadata.html b/docs/dev/generated/skbio.io.format.sample_metadata.html
index a1e2d87d3..616a02b9c 100644
--- a/docs/dev/generated/skbio.io.format.sample_metadata.html
+++ b/docs/dev/generated/skbio.io.format.sample_metadata.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.format.stockholm.html b/docs/dev/generated/skbio.io.format.stockholm.html
index 814e6923d..77591ab90 100644
--- a/docs/dev/generated/skbio.io.format.stockholm.html
+++ b/docs/dev/generated/skbio.io.format.stockholm.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.format.taxdump.html b/docs/dev/generated/skbio.io.format.taxdump.html
index 0395dc0e9..7edb0df8f 100644
--- a/docs/dev/generated/skbio.io.format.taxdump.html
+++ b/docs/dev/generated/skbio.io.format.taxdump.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.DuplicateRegistrationError.html b/docs/dev/generated/skbio.io.registry.DuplicateRegistrationError.html
index 2c5640b04..a092023b4 100644
--- a/docs/dev/generated/skbio.io.registry.DuplicateRegistrationError.html
+++ b/docs/dev/generated/skbio.io.registry.DuplicateRegistrationError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.Format.__eq__.html b/docs/dev/generated/skbio.io.registry.Format.__eq__.html
index 78063904c..2ecdb90f1 100644
--- a/docs/dev/generated/skbio.io.registry.Format.__eq__.html
+++ b/docs/dev/generated/skbio.io.registry.Format.__eq__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.Format.__ge__.html b/docs/dev/generated/skbio.io.registry.Format.__ge__.html
index 8ff90217c..becc5325b 100644
--- a/docs/dev/generated/skbio.io.registry.Format.__ge__.html
+++ b/docs/dev/generated/skbio.io.registry.Format.__ge__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.Format.__getstate__.html b/docs/dev/generated/skbio.io.registry.Format.__getstate__.html
index 5cc7ab8a1..a53a8fe88 100644
--- a/docs/dev/generated/skbio.io.registry.Format.__getstate__.html
+++ b/docs/dev/generated/skbio.io.registry.Format.__getstate__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.Format.__gt__.html b/docs/dev/generated/skbio.io.registry.Format.__gt__.html
index 797d138eb..010be2016 100644
--- a/docs/dev/generated/skbio.io.registry.Format.__gt__.html
+++ b/docs/dev/generated/skbio.io.registry.Format.__gt__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.Format.__hash__.html b/docs/dev/generated/skbio.io.registry.Format.__hash__.html
index c02b1c194..98cec0d2b 100644
--- a/docs/dev/generated/skbio.io.registry.Format.__hash__.html
+++ b/docs/dev/generated/skbio.io.registry.Format.__hash__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.Format.__le__.html b/docs/dev/generated/skbio.io.registry.Format.__le__.html
index 2b0a9d03b..e1f0403aa 100644
--- a/docs/dev/generated/skbio.io.registry.Format.__le__.html
+++ b/docs/dev/generated/skbio.io.registry.Format.__le__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.Format.__lt__.html b/docs/dev/generated/skbio.io.registry.Format.__lt__.html
index 2786a79b4..3f073d86f 100644
--- a/docs/dev/generated/skbio.io.registry.Format.__lt__.html
+++ b/docs/dev/generated/skbio.io.registry.Format.__lt__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.Format.__ne__.html b/docs/dev/generated/skbio.io.registry.Format.__ne__.html
index 7b2aa17b8..b173d93fb 100644
--- a/docs/dev/generated/skbio.io.registry.Format.__ne__.html
+++ b/docs/dev/generated/skbio.io.registry.Format.__ne__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.Format.__str__.html b/docs/dev/generated/skbio.io.registry.Format.__str__.html
index 9e21166ad..86da4b43c 100644
--- a/docs/dev/generated/skbio.io.registry.Format.__str__.html
+++ b/docs/dev/generated/skbio.io.registry.Format.__str__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.Format.html b/docs/dev/generated/skbio.io.registry.Format.html
index d2a7d83eb..fda753b4f 100644
--- a/docs/dev/generated/skbio.io.registry.Format.html
+++ b/docs/dev/generated/skbio.io.registry.Format.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.Format.reader.html b/docs/dev/generated/skbio.io.registry.Format.reader.html
index d121d0877..17c930b63 100644
--- a/docs/dev/generated/skbio.io.registry.Format.reader.html
+++ b/docs/dev/generated/skbio.io.registry.Format.reader.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.Format.sniffer.html b/docs/dev/generated/skbio.io.registry.Format.sniffer.html
index 3d3bd6af5..64ed700c3 100644
--- a/docs/dev/generated/skbio.io.registry.Format.sniffer.html
+++ b/docs/dev/generated/skbio.io.registry.Format.sniffer.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.Format.writer.html b/docs/dev/generated/skbio.io.registry.Format.writer.html
index 9dfad39cc..1baa25e1a 100644
--- a/docs/dev/generated/skbio.io.registry.Format.writer.html
+++ b/docs/dev/generated/skbio.io.registry.Format.writer.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.__eq__.html b/docs/dev/generated/skbio.io.registry.IORegistry.__eq__.html
index 4d7dc56fb..c2aae23a1 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.__eq__.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.__eq__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.__ge__.html b/docs/dev/generated/skbio.io.registry.IORegistry.__ge__.html
index fb5c00fe8..0de509e53 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.__ge__.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.__ge__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.__getstate__.html b/docs/dev/generated/skbio.io.registry.IORegistry.__getstate__.html
index 4f07f9da3..b9959a254 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.__getstate__.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.__getstate__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.__gt__.html b/docs/dev/generated/skbio.io.registry.IORegistry.__gt__.html
index bcc8e5f7a..6129e009e 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.__gt__.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.__gt__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.__hash__.html b/docs/dev/generated/skbio.io.registry.IORegistry.__hash__.html
index 4fbdee9f4..4be4d96e6 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.__hash__.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.__hash__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.__le__.html b/docs/dev/generated/skbio.io.registry.IORegistry.__le__.html
index a2531b943..6161131d0 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.__le__.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.__le__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.__lt__.html b/docs/dev/generated/skbio.io.registry.IORegistry.__lt__.html
index 350c89859..ef3f81967 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.__lt__.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.__lt__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.__ne__.html b/docs/dev/generated/skbio.io.registry.IORegistry.__ne__.html
index d9e8dd3bb..3351dc9dd 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.__ne__.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.__ne__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.__str__.html b/docs/dev/generated/skbio.io.registry.IORegistry.__str__.html
index 74876d9a1..5f426f42d 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.__str__.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.__str__.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.add_format.html b/docs/dev/generated/skbio.io.registry.IORegistry.add_format.html
index f737ec3ae..b30e79240 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.add_format.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.add_format.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.create_format.html b/docs/dev/generated/skbio.io.registry.IORegistry.create_format.html
index 0f64ba807..b43857483 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.create_format.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.create_format.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.get_reader.html b/docs/dev/generated/skbio.io.registry.IORegistry.get_reader.html
index 76afd9d00..c8e50db54 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.get_reader.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.get_reader.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.get_sniffer.html b/docs/dev/generated/skbio.io.registry.IORegistry.get_sniffer.html
index 2e7715ad4..a2ae30561 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.get_sniffer.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.get_sniffer.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.get_writer.html b/docs/dev/generated/skbio.io.registry.IORegistry.get_writer.html
index 2de806767..96c33d67a 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.get_writer.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.get_writer.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.html b/docs/dev/generated/skbio.io.registry.IORegistry.html
index dc948a669..b94a9c55c 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.list_read_formats.html b/docs/dev/generated/skbio.io.registry.IORegistry.list_read_formats.html
index 5d51916e5..08959bf11 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.list_read_formats.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.list_read_formats.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.list_write_formats.html b/docs/dev/generated/skbio.io.registry.IORegistry.list_write_formats.html
index 1da616afb..ca978a381 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.list_write_formats.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.list_write_formats.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.monkey_patch.html b/docs/dev/generated/skbio.io.registry.IORegistry.monkey_patch.html
index 37c86717e..68d402963 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.monkey_patch.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.monkey_patch.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.read.html b/docs/dev/generated/skbio.io.registry.IORegistry.read.html
index 4943fdf51..262a7ae3a 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.read.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.read.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.sniff.html b/docs/dev/generated/skbio.io.registry.IORegistry.sniff.html
index 6027c9851..110880b0c 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.sniff.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.sniff.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.IORegistry.write.html b/docs/dev/generated/skbio.io.registry.IORegistry.write.html
index 271ad6031..c297adcc4 100644
--- a/docs/dev/generated/skbio.io.registry.IORegistry.write.html
+++ b/docs/dev/generated/skbio.io.registry.IORegistry.write.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.InvalidRegistrationError.html b/docs/dev/generated/skbio.io.registry.InvalidRegistrationError.html
index b7d2047b2..b7ed9836f 100644
--- a/docs/dev/generated/skbio.io.registry.InvalidRegistrationError.html
+++ b/docs/dev/generated/skbio.io.registry.InvalidRegistrationError.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.create_format.html b/docs/dev/generated/skbio.io.registry.create_format.html
index 4aaf07710..6c8ace605 100644
--- a/docs/dev/generated/skbio.io.registry.create_format.html
+++ b/docs/dev/generated/skbio.io.registry.create_format.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.html b/docs/dev/generated/skbio.io.registry.html
index 7c5c1f37a..6975f56d6 100644
--- a/docs/dev/generated/skbio.io.registry.html
+++ b/docs/dev/generated/skbio.io.registry.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.read.html b/docs/dev/generated/skbio.io.registry.read.html
index 190efd8c2..1b658a103 100644
--- a/docs/dev/generated/skbio.io.registry.read.html
+++ b/docs/dev/generated/skbio.io.registry.read.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.sniff.html b/docs/dev/generated/skbio.io.registry.sniff.html
index 682aff9b2..826074b88 100644
--- a/docs/dev/generated/skbio.io.registry.sniff.html
+++ b/docs/dev/generated/skbio.io.registry.sniff.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.registry.write.html b/docs/dev/generated/skbio.io.registry.write.html
index 78d888bea..2e2ad679c 100644
--- a/docs/dev/generated/skbio.io.registry.write.html
+++ b/docs/dev/generated/skbio.io.registry.write.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.util.html b/docs/dev/generated/skbio.io.util.html
index 45c2be6c7..9a441bc11 100644
--- a/docs/dev/generated/skbio.io.util.html
+++ b/docs/dev/generated/skbio.io.util.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.util.open.html b/docs/dev/generated/skbio.io.util.open.html
index 04154015e..f4810dc6b 100644
--- a/docs/dev/generated/skbio.io.util.open.html
+++ b/docs/dev/generated/skbio.io.util.open.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.util.open_file.html b/docs/dev/generated/skbio.io.util.open_file.html
index 973a4f0d4..8ceb357bf 100644
--- a/docs/dev/generated/skbio.io.util.open_file.html
+++ b/docs/dev/generated/skbio.io.util.open_file.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/generated/skbio.io.util.open_files.html b/docs/dev/generated/skbio.io.util.open_files.html
index 8cfcdcac3..f2cb99273 100644
--- a/docs/dev/generated/skbio.io.util.open_files.html
+++ b/docs/dev/generated/skbio.io.util.open_files.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
diff --git a/docs/dev/genindex.html b/docs/dev/genindex.html
index ac949606c..0c29e3abb 100644
--- a/docs/dev/genindex.html
+++ b/docs/dev/genindex.html
@@ -2190,6 +2190,8 @@ <h2 id="M">M</h2>
         <li><a href="io.html#module-skbio.io">skbio.io</a>
 </li>
         <li><a href="generated/skbio.io.format.binary_dm.html#module-skbio.io.format.binary_dm">skbio.io.format.binary_dm</a>
+</li>
+        <li><a href="generated/skbio.io.format.biom.html#module-skbio.io.format.biom">skbio.io.format.biom</a>
 </li>
         <li><a href="generated/skbio.io.format.blast6.html#module-skbio.io.format.blast6">skbio.io.format.blast6</a>
 </li>
@@ -2556,6 +2558,13 @@ <h2 id="S">S</h2>
 
       <ul>
         <li><a href="generated/skbio.io.format.binary_dm.html#module-skbio.io.format.binary_dm">module</a>
+</li>
+      </ul></li>
+      <li>
+    skbio.io.format.biom
+
+      <ul>
+        <li><a href="generated/skbio.io.format.biom.html#module-skbio.io.format.biom">module</a>
 </li>
       </ul></li>
       <li>
@@ -2649,6 +2658,8 @@ <h2 id="S">S</h2>
         <li><a href="generated/skbio.io.format.qseq.html#module-skbio.io.format.qseq">module</a>
 </li>
       </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li>
     skbio.io.format.sample_metadata
 
@@ -2656,8 +2667,6 @@ <h2 id="S">S</h2>
         <li><a href="generated/skbio.io.format.sample_metadata.html#module-skbio.io.format.sample_metadata">module</a>
 </li>
       </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li>
     skbio.io.format.stockholm
 
diff --git a/docs/dev/io.html b/docs/dev/io.html
index 4d242d1b5..37a732dc9 100644
--- a/docs/dev/io.html
+++ b/docs/dev/io.html
@@ -601,6 +601,7 @@
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="generated/skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="generated/skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="generated/skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="generated/skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>
 
@@ -716,52 +717,55 @@ <h2>Supported file formats<a class="headerlink" href="#supported-file-formats" t
 <tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.binary_dm.html#module-skbio.io.format.binary_dm" title="skbio.io.format.binary_dm"><code class="xref py py-obj docutils literal notranslate"><span class="pre">binary_dm</span></code></a></p></td>
 <td><p>Simple binary dissimilarity matrix format (skbio.io.format.binary_dm)</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.blast6.html#module-skbio.io.format.blast6" title="skbio.io.format.blast6"><code class="xref py py-obj docutils literal notranslate"><span class="pre">blast6</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.biom.html#module-skbio.io.format.biom" title="skbio.io.format.biom"><code class="xref py py-obj docutils literal notranslate"><span class="pre">biom</span></code></a></p></td>
+<td><p>BIOM-Format (skbio.io.format.biom)</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.blast6.html#module-skbio.io.format.blast6" title="skbio.io.format.blast6"><code class="xref py py-obj docutils literal notranslate"><span class="pre">blast6</span></code></a></p></td>
 <td><p>BLAST+6 format (skbio.io.format.blast6)</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.blast7.html#module-skbio.io.format.blast7" title="skbio.io.format.blast7"><code class="xref py py-obj docutils literal notranslate"><span class="pre">blast7</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.blast7.html#module-skbio.io.format.blast7" title="skbio.io.format.blast7"><code class="xref py py-obj docutils literal notranslate"><span class="pre">blast7</span></code></a></p></td>
 <td><p>BLAST+7 format (skbio.io.format.blast7)</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.clustal.html#module-skbio.io.format.clustal" title="skbio.io.format.clustal"><code class="xref py py-obj docutils literal notranslate"><span class="pre">clustal</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.clustal.html#module-skbio.io.format.clustal" title="skbio.io.format.clustal"><code class="xref py py-obj docutils literal notranslate"><span class="pre">clustal</span></code></a></p></td>
 <td><p>Clustal format (skbio.io.format.clustal)</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.embl.html#module-skbio.io.format.embl" title="skbio.io.format.embl"><code class="xref py py-obj docutils literal notranslate"><span class="pre">embl</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.embl.html#module-skbio.io.format.embl" title="skbio.io.format.embl"><code class="xref py py-obj docutils literal notranslate"><span class="pre">embl</span></code></a></p></td>
 <td><p>EMBL format (skbio.io.format.embl)</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.fasta.html#module-skbio.io.format.fasta" title="skbio.io.format.fasta"><code class="xref py py-obj docutils literal notranslate"><span class="pre">fasta</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.fasta.html#module-skbio.io.format.fasta" title="skbio.io.format.fasta"><code class="xref py py-obj docutils literal notranslate"><span class="pre">fasta</span></code></a></p></td>
 <td><p>FASTA/QUAL format (skbio.io.format.fasta)</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.fastq.html#module-skbio.io.format.fastq" title="skbio.io.format.fastq"><code class="xref py py-obj docutils literal notranslate"><span class="pre">fastq</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.fastq.html#module-skbio.io.format.fastq" title="skbio.io.format.fastq"><code class="xref py py-obj docutils literal notranslate"><span class="pre">fastq</span></code></a></p></td>
 <td><p>FASTQ format (skbio.io.format.fastq)</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.genbank.html#module-skbio.io.format.genbank" title="skbio.io.format.genbank"><code class="xref py py-obj docutils literal notranslate"><span class="pre">genbank</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.genbank.html#module-skbio.io.format.genbank" title="skbio.io.format.genbank"><code class="xref py py-obj docutils literal notranslate"><span class="pre">genbank</span></code></a></p></td>
 <td><p>GenBank format (skbio.io.format.genbank)</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.gff3.html#module-skbio.io.format.gff3" title="skbio.io.format.gff3"><code class="xref py py-obj docutils literal notranslate"><span class="pre">gff3</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.gff3.html#module-skbio.io.format.gff3" title="skbio.io.format.gff3"><code class="xref py py-obj docutils literal notranslate"><span class="pre">gff3</span></code></a></p></td>
 <td><p>GFF3 format (skbio.io.format.gff3)</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.lsmat.html#module-skbio.io.format.lsmat" title="skbio.io.format.lsmat"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lsmat</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.lsmat.html#module-skbio.io.format.lsmat" title="skbio.io.format.lsmat"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lsmat</span></code></a></p></td>
 <td><p>Labeled square matrix format (skbio.io.format.lsmat)</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.newick.html#module-skbio.io.format.newick" title="skbio.io.format.newick"><code class="xref py py-obj docutils literal notranslate"><span class="pre">newick</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.newick.html#module-skbio.io.format.newick" title="skbio.io.format.newick"><code class="xref py py-obj docutils literal notranslate"><span class="pre">newick</span></code></a></p></td>
 <td><p>Newick format (skbio.io.format.newick)</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.ordination.html#module-skbio.io.format.ordination" title="skbio.io.format.ordination"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ordination</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.ordination.html#module-skbio.io.format.ordination" title="skbio.io.format.ordination"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ordination</span></code></a></p></td>
 <td><p>Ordination results format (skbio.io.format.ordination)</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.phylip.html#module-skbio.io.format.phylip" title="skbio.io.format.phylip"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phylip</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.phylip.html#module-skbio.io.format.phylip" title="skbio.io.format.phylip"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phylip</span></code></a></p></td>
 <td><p>PHYLIP multiple sequence alignment format (skbio.io.format.phylip)</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.qseq.html#module-skbio.io.format.qseq" title="skbio.io.format.qseq"><code class="xref py py-obj docutils literal notranslate"><span class="pre">qseq</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.qseq.html#module-skbio.io.format.qseq" title="skbio.io.format.qseq"><code class="xref py py-obj docutils literal notranslate"><span class="pre">qseq</span></code></a></p></td>
 <td><p>QSeq format (skbio.io.format.qseq)</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.stockholm.html#module-skbio.io.format.stockholm" title="skbio.io.format.stockholm"><code class="xref py py-obj docutils literal notranslate"><span class="pre">stockholm</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.stockholm.html#module-skbio.io.format.stockholm" title="skbio.io.format.stockholm"><code class="xref py py-obj docutils literal notranslate"><span class="pre">stockholm</span></code></a></p></td>
 <td><p>Stockholm format (skbio.io.format.stockholm)</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.taxdump.html#module-skbio.io.format.taxdump" title="skbio.io.format.taxdump"><code class="xref py py-obj docutils literal notranslate"><span class="pre">taxdump</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.taxdump.html#module-skbio.io.format.taxdump" title="skbio.io.format.taxdump"><code class="xref py py-obj docutils literal notranslate"><span class="pre">taxdump</span></code></a></p></td>
 <td><p>Taxdump format (skbio.io.format.taxdump)</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.io.format.sample_metadata.html#module-skbio.io.format.sample_metadata" title="skbio.io.format.sample_metadata"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sample_metadata</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/skbio.io.format.sample_metadata.html#module-skbio.io.format.sample_metadata" title="skbio.io.format.sample_metadata"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sample_metadata</span></code></a></p></td>
 <td><p>Sample Metadata object ported over from qiime2.</p></td>
 </tr>
 </tbody>
diff --git a/docs/dev/objects.inv b/docs/dev/objects.inv
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diff --git a/docs/dev/py-modindex.html b/docs/dev/py-modindex.html
index 88ab35e40..544339a4c 100644
--- a/docs/dev/py-modindex.html
+++ b/docs/dev/py-modindex.html
@@ -662,6 +662,11 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="generated/skbio.io.format.binary_dm.html#module-skbio.io.format.binary_dm"><code class="xref">skbio.io.format.binary_dm</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="generated/skbio.io.format.biom.html#module-skbio.io.format.biom"><code class="xref">skbio.io.format.biom</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
diff --git a/docs/dev/searchindex.js b/docs/dev/searchindex.js
index 84a82e514..e1ca28692 100644
--- a/docs/dev/searchindex.js
+++ b/docs/dev/searchindex.js
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"generated/skbio.workflow.Workflow.__lt__.rst", "generated/skbio.workflow.Workflow.__ne__.rst", "generated/skbio.workflow.Workflow.__str__.rst", "generated/skbio.workflow.Workflow.initialize_state.rst", "generated/skbio.workflow.method.rst", "generated/skbio.workflow.method.__call__.rst", "generated/skbio.workflow.method.__eq__.rst", "generated/skbio.workflow.method.__ge__.rst", "generated/skbio.workflow.method.__getstate__.rst", "generated/skbio.workflow.method.__gt__.rst", "generated/skbio.workflow.method.__hash__.rst", "generated/skbio.workflow.method.__le__.rst", "generated/skbio.workflow.method.__lt__.rst", "generated/skbio.workflow.method.__ne__.rst", "generated/skbio.workflow.method.__str__.rst", "generated/skbio.workflow.requires.rst", "generated/skbio.workflow.requires.__call__.rst", "generated/skbio.workflow.requires.__eq__.rst", "generated/skbio.workflow.requires.__ge__.rst", "generated/skbio.workflow.requires.__getstate__.rst", "generated/skbio.workflow.requires.__gt__.rst", "generated/skbio.workflow.requires.__hash__.rst", "generated/skbio.workflow.requires.__le__.rst", "generated/skbio.workflow.requires.__lt__.rst", "generated/skbio.workflow.requires.__ne__.rst", "generated/skbio.workflow.requires.__str__.rst", "index.rst", "io.rst", "metadata.rst", "sequence.rst", "stats.rst", "tree.rst", "util.rst", "workflow.rst"], "titles": ["Alignments (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.alignment</span></code>)", "Diversity calculations (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.diversity</span></code>)", "skbio.alignment.AlignmentStructure", "skbio.alignment.AlignmentStructure.__eq__", "skbio.alignment.AlignmentStructure.__ge__", "skbio.alignment.AlignmentStructure.__getitem__", "skbio.alignment.AlignmentStructure.__getstate__", "skbio.alignment.AlignmentStructure.__gt__", "skbio.alignment.AlignmentStructure.__hash__", "skbio.alignment.AlignmentStructure.__le__", "skbio.alignment.AlignmentStructure.__lt__", "skbio.alignment.AlignmentStructure.__ne__", "skbio.alignment.AlignmentStructure.__setstate__", "skbio.alignment.AlignmentStructure.__str__", "skbio.alignment.AlignmentStructure.is_zero_based", "skbio.alignment.AlignmentStructure.set_zero_based", "skbio.alignment.StripedSmithWaterman", "skbio.alignment.StripedSmithWaterman.__call__", "skbio.alignment.StripedSmithWaterman.__eq__", "skbio.alignment.StripedSmithWaterman.__ge__", "skbio.alignment.StripedSmithWaterman.__getstate__", "skbio.alignment.StripedSmithWaterman.__gt__", "skbio.alignment.StripedSmithWaterman.__hash__", "skbio.alignment.StripedSmithWaterman.__le__", "skbio.alignment.StripedSmithWaterman.__lt__", "skbio.alignment.StripedSmithWaterman.__ne__", "skbio.alignment.StripedSmithWaterman.__setstate__", "skbio.alignment.StripedSmithWaterman.__str__", "skbio.alignment.TabularMSA", "skbio.alignment.TabularMSA.__bool__", "skbio.alignment.TabularMSA.__contains__", "skbio.alignment.TabularMSA.__copy__", "skbio.alignment.TabularMSA.__deepcopy__", "skbio.alignment.TabularMSA.__eq__", "skbio.alignment.TabularMSA.__ge__", "skbio.alignment.TabularMSA.__getitem__", "skbio.alignment.TabularMSA.__getstate__", "skbio.alignment.TabularMSA.__gt__", "skbio.alignment.TabularMSA.__iter__", "skbio.alignment.TabularMSA.__le__", "skbio.alignment.TabularMSA.__len__", "skbio.alignment.TabularMSA.__lt__", "skbio.alignment.TabularMSA.__ne__", "skbio.alignment.TabularMSA.__reversed__", "skbio.alignment.TabularMSA.__str__", "skbio.alignment.TabularMSA.append", "skbio.alignment.TabularMSA.consensus", "skbio.alignment.TabularMSA.conservation", "skbio.alignment.TabularMSA.extend", "skbio.alignment.TabularMSA.from_dict", "skbio.alignment.TabularMSA.gap_frequencies", "skbio.alignment.TabularMSA.has_metadata", "skbio.alignment.TabularMSA.has_positional_metadata", "skbio.alignment.TabularMSA.iter_positions", "skbio.alignment.TabularMSA.join", "skbio.alignment.TabularMSA.read", "skbio.alignment.TabularMSA.reassign_index", "skbio.alignment.TabularMSA.sort", "skbio.alignment.TabularMSA.to_dict", "skbio.alignment.TabularMSA.write", "skbio.alignment.global_pairwise_align", "skbio.alignment.global_pairwise_align_nucleotide", "skbio.alignment.global_pairwise_align_protein", "skbio.alignment.local_pairwise_align", "skbio.alignment.local_pairwise_align_nucleotide", "skbio.alignment.local_pairwise_align_protein", "skbio.alignment.local_pairwise_align_ssw", "skbio.alignment.make_identity_substitution_matrix", "Alpha diversity measures (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.diversity.alpha</span></code>)", "skbio.diversity.alpha.ace", "skbio.diversity.alpha.berger_parker_d", "skbio.diversity.alpha.brillouin_d", "skbio.diversity.alpha.chao1", "skbio.diversity.alpha.chao1_ci", "skbio.diversity.alpha.dominance", "skbio.diversity.alpha.doubles", "skbio.diversity.alpha.enspie", "skbio.diversity.alpha.esty_ci", "skbio.diversity.alpha.faith_pd", "skbio.diversity.alpha.fisher_alpha", "skbio.diversity.alpha.gini_index", "skbio.diversity.alpha.goods_coverage", "skbio.diversity.alpha.heip_e", "skbio.diversity.alpha.kempton_taylor_q", "skbio.diversity.alpha.lladser_ci", "skbio.diversity.alpha.lladser_pe", "skbio.diversity.alpha.margalef", "skbio.diversity.alpha.mcintosh_d", "skbio.diversity.alpha.mcintosh_e", "skbio.diversity.alpha.menhinick", "skbio.diversity.alpha.michaelis_menten_fit", "skbio.diversity.alpha.observed_features", "skbio.diversity.alpha.observed_otus", "skbio.diversity.alpha.osd", "skbio.diversity.alpha.phydiv", "skbio.diversity.alpha.pielou_e", "skbio.diversity.alpha.robbins", "skbio.diversity.alpha.shannon", "skbio.diversity.alpha.simpson", "skbio.diversity.alpha.simpson_e", "skbio.diversity.alpha.singles", "skbio.diversity.alpha.sobs", "skbio.diversity.alpha.strong", "skbio.diversity.alpha_diversity", "Beta diversity measures (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.diversity.beta</span></code>)", "skbio.diversity.beta.unweighted_unifrac", "skbio.diversity.beta.weighted_unifrac", "skbio.diversity.beta_diversity", "skbio.diversity.block_beta_diversity", "skbio.diversity.get_alpha_diversity_metrics", "skbio.diversity.get_beta_diversity_metrics", "skbio.diversity.partial_beta_diversity", "skbio.io.ArgumentOverrideWarning", "skbio.io.BLAST7FormatError", "skbio.io.ClustalFormatError", "skbio.io.EMBLFormatError", "skbio.io.FASTAFormatError", "skbio.io.FASTQFormatError", "skbio.io.FileFormatError", "skbio.io.FormatIdentificationWarning", "skbio.io.GFF3FormatError", "skbio.io.GenBankFormatError", "skbio.io.IOSourceError", "skbio.io.LSMatFormatError", "skbio.io.NewickFormatError", "skbio.io.OrdinationFormatError", "skbio.io.PhylipFormatError", "skbio.io.QSeqFormatError", "skbio.io.QUALFormatError", "skbio.io.StockholmFormatError", "skbio.io.UnrecognizedFormatError", "Simple binary dissimilarity matrix format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.binary_dm</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>)", "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.DuplicateRegistrationError", "skbio.io.registry.Format", "skbio.io.registry.Format.__eq__", "skbio.io.registry.Format.__ge__", "skbio.io.registry.Format.__getstate__", "skbio.io.registry.Format.__gt__", "skbio.io.registry.Format.__hash__", "skbio.io.registry.Format.__le__", "skbio.io.registry.Format.__lt__", "skbio.io.registry.Format.__ne__", "skbio.io.registry.Format.__str__", "skbio.io.registry.Format.reader", "skbio.io.registry.Format.sniffer", "skbio.io.registry.Format.writer", "skbio.io.registry.IORegistry", "skbio.io.registry.IORegistry.__eq__", "skbio.io.registry.IORegistry.__ge__", "skbio.io.registry.IORegistry.__getstate__", "skbio.io.registry.IORegistry.__gt__", "skbio.io.registry.IORegistry.__hash__", "skbio.io.registry.IORegistry.__le__", "skbio.io.registry.IORegistry.__lt__", "skbio.io.registry.IORegistry.__ne__", "skbio.io.registry.IORegistry.__str__", "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.InvalidRegistrationError", "skbio.io.registry.create_format", "skbio.io.registry.read", "skbio.io.registry.sniff", "skbio.io.registry.write", "I/O utils (<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.Interval", "skbio.metadata.Interval.__eq__", "skbio.metadata.Interval.__ge__", "skbio.metadata.Interval.__getstate__", "skbio.metadata.Interval.__gt__", "skbio.metadata.Interval.__le__", "skbio.metadata.Interval.__lt__", "skbio.metadata.Interval.__ne__", "skbio.metadata.Interval.__str__", "skbio.metadata.Interval.drop", "skbio.metadata.IntervalMetadata", "skbio.metadata.IntervalMetadata.__copy__", "skbio.metadata.IntervalMetadata.__deepcopy__", "skbio.metadata.IntervalMetadata.__eq__", "skbio.metadata.IntervalMetadata.__ge__", "skbio.metadata.IntervalMetadata.__getstate__", "skbio.metadata.IntervalMetadata.__gt__", "skbio.metadata.IntervalMetadata.__le__", "skbio.metadata.IntervalMetadata.__lt__", "skbio.metadata.IntervalMetadata.__ne__", "skbio.metadata.IntervalMetadata.__str__", "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.sequence.DNA", "skbio.sequence.DNA.__bool__", "skbio.sequence.DNA.__contains__", "skbio.sequence.DNA.__copy__", "skbio.sequence.DNA.__deepcopy__", "skbio.sequence.DNA.__eq__", "skbio.sequence.DNA.__ge__", "skbio.sequence.DNA.__getitem__", "skbio.sequence.DNA.__getstate__", "skbio.sequence.DNA.__gt__", "skbio.sequence.DNA.__iter__", "skbio.sequence.DNA.__le__", "skbio.sequence.DNA.__len__", "skbio.sequence.DNA.__lt__", "skbio.sequence.DNA.__ne__", "skbio.sequence.DNA.__reversed__", "skbio.sequence.DNA.__str__", "skbio.sequence.DNA.complement", "skbio.sequence.DNA.concat", "skbio.sequence.DNA.count", "skbio.sequence.DNA.definites", "skbio.sequence.DNA.degap", "skbio.sequence.DNA.degenerates", "skbio.sequence.DNA.distance", "skbio.sequence.DNA.expand_degenerates", "skbio.sequence.DNA.find_motifs", "skbio.sequence.DNA.find_with_regex", "skbio.sequence.DNA.frequencies", "skbio.sequence.DNA.gaps", "skbio.sequence.DNA.gc_content", "skbio.sequence.DNA.gc_frequency", "skbio.sequence.DNA.has_definites", "skbio.sequence.DNA.has_degenerates", "skbio.sequence.DNA.has_gaps", "skbio.sequence.DNA.has_interval_metadata", "skbio.sequence.DNA.has_metadata", "skbio.sequence.DNA.has_nondegenerates", "skbio.sequence.DNA.has_positional_metadata", "skbio.sequence.DNA.index", "skbio.sequence.DNA.is_reverse_complement", "skbio.sequence.DNA.iter_contiguous", "skbio.sequence.DNA.iter_kmers", "skbio.sequence.DNA.kmer_frequencies", "skbio.sequence.DNA.lowercase", "skbio.sequence.DNA.match_frequency", "skbio.sequence.DNA.matches", "skbio.sequence.DNA.mismatch_frequency", "skbio.sequence.DNA.mismatches", "skbio.sequence.DNA.nondegenerates", "skbio.sequence.DNA.read", "skbio.sequence.DNA.replace", "skbio.sequence.DNA.reverse_complement", "skbio.sequence.DNA.to_definites", "skbio.sequence.DNA.to_indices", "skbio.sequence.DNA.to_regex", "skbio.sequence.DNA.transcribe", "skbio.sequence.DNA.translate", "skbio.sequence.DNA.translate_six_frames", "skbio.sequence.DNA.write", "skbio.sequence.GeneticCode", "skbio.sequence.GeneticCode.__eq__", "skbio.sequence.GeneticCode.__ge__", "skbio.sequence.GeneticCode.__getstate__", "skbio.sequence.GeneticCode.__gt__", "skbio.sequence.GeneticCode.__le__", "skbio.sequence.GeneticCode.__lt__", "skbio.sequence.GeneticCode.__ne__", "skbio.sequence.GeneticCode.__str__", "skbio.sequence.GeneticCode.from_ncbi", "skbio.sequence.GeneticCode.translate", "skbio.sequence.GeneticCode.translate_six_frames", "skbio.sequence.GrammaredSequence", "skbio.sequence.GrammaredSequence.__bool__", "skbio.sequence.GrammaredSequence.__contains__", "skbio.sequence.GrammaredSequence.__copy__", "skbio.sequence.GrammaredSequence.__deepcopy__", "skbio.sequence.GrammaredSequence.__eq__", "skbio.sequence.GrammaredSequence.__ge__", "skbio.sequence.GrammaredSequence.__getitem__", "skbio.sequence.GrammaredSequence.__getstate__", "skbio.sequence.GrammaredSequence.__gt__", "skbio.sequence.GrammaredSequence.__iter__", "skbio.sequence.GrammaredSequence.__le__", "skbio.sequence.GrammaredSequence.__len__", "skbio.sequence.GrammaredSequence.__lt__", "skbio.sequence.GrammaredSequence.__ne__", "skbio.sequence.GrammaredSequence.__reversed__", "skbio.sequence.GrammaredSequence.__str__", "skbio.sequence.GrammaredSequence.concat", "skbio.sequence.GrammaredSequence.count", "skbio.sequence.GrammaredSequence.definites", "skbio.sequence.GrammaredSequence.degap", "skbio.sequence.GrammaredSequence.degenerates", "skbio.sequence.GrammaredSequence.distance", "skbio.sequence.GrammaredSequence.expand_degenerates", "skbio.sequence.GrammaredSequence.find_motifs", "skbio.sequence.GrammaredSequence.find_with_regex", "skbio.sequence.GrammaredSequence.frequencies", "skbio.sequence.GrammaredSequence.gaps", "skbio.sequence.GrammaredSequence.has_definites", "skbio.sequence.GrammaredSequence.has_degenerates", "skbio.sequence.GrammaredSequence.has_gaps", "skbio.sequence.GrammaredSequence.has_interval_metadata", "skbio.sequence.GrammaredSequence.has_metadata", "skbio.sequence.GrammaredSequence.has_nondegenerates", "skbio.sequence.GrammaredSequence.has_positional_metadata", "skbio.sequence.GrammaredSequence.index", "skbio.sequence.GrammaredSequence.iter_contiguous", "skbio.sequence.GrammaredSequence.iter_kmers", "skbio.sequence.GrammaredSequence.kmer_frequencies", "skbio.sequence.GrammaredSequence.lowercase", "skbio.sequence.GrammaredSequence.match_frequency", "skbio.sequence.GrammaredSequence.matches", "skbio.sequence.GrammaredSequence.mismatch_frequency", "skbio.sequence.GrammaredSequence.mismatches", "skbio.sequence.GrammaredSequence.nondegenerates", "skbio.sequence.GrammaredSequence.read", "skbio.sequence.GrammaredSequence.replace", "skbio.sequence.GrammaredSequence.to_definites", "skbio.sequence.GrammaredSequence.to_indices", "skbio.sequence.GrammaredSequence.to_regex", "skbio.sequence.GrammaredSequence.write", "skbio.sequence.Protein", "skbio.sequence.Protein.__bool__", "skbio.sequence.Protein.__contains__", "skbio.sequence.Protein.__copy__", "skbio.sequence.Protein.__deepcopy__", "skbio.sequence.Protein.__eq__", "skbio.sequence.Protein.__ge__", "skbio.sequence.Protein.__getitem__", "skbio.sequence.Protein.__getstate__", "skbio.sequence.Protein.__gt__", "skbio.sequence.Protein.__iter__", "skbio.sequence.Protein.__le__", "skbio.sequence.Protein.__len__", "skbio.sequence.Protein.__lt__", "skbio.sequence.Protein.__ne__", "skbio.sequence.Protein.__reversed__", "skbio.sequence.Protein.__str__", "skbio.sequence.Protein.concat", "skbio.sequence.Protein.count", "skbio.sequence.Protein.definites", "skbio.sequence.Protein.degap", "skbio.sequence.Protein.degenerates", "skbio.sequence.Protein.distance", "skbio.sequence.Protein.expand_degenerates", "skbio.sequence.Protein.find_motifs", "skbio.sequence.Protein.find_with_regex", "skbio.sequence.Protein.frequencies", "skbio.sequence.Protein.gaps", "skbio.sequence.Protein.has_definites", "skbio.sequence.Protein.has_degenerates", "skbio.sequence.Protein.has_gaps", "skbio.sequence.Protein.has_interval_metadata", "skbio.sequence.Protein.has_metadata", "skbio.sequence.Protein.has_nondegenerates", "skbio.sequence.Protein.has_positional_metadata", "skbio.sequence.Protein.has_stops", "skbio.sequence.Protein.index", "skbio.sequence.Protein.iter_contiguous", "skbio.sequence.Protein.iter_kmers", "skbio.sequence.Protein.kmer_frequencies", "skbio.sequence.Protein.lowercase", "skbio.sequence.Protein.match_frequency", "skbio.sequence.Protein.matches", "skbio.sequence.Protein.mismatch_frequency", "skbio.sequence.Protein.mismatches", "skbio.sequence.Protein.nondegenerates", "skbio.sequence.Protein.read", "skbio.sequence.Protein.replace", "skbio.sequence.Protein.stops", "skbio.sequence.Protein.to_definites", "skbio.sequence.Protein.to_indices", "skbio.sequence.Protein.to_regex", "skbio.sequence.Protein.write", "skbio.sequence.RNA", "skbio.sequence.RNA.__bool__", "skbio.sequence.RNA.__contains__", "skbio.sequence.RNA.__copy__", "skbio.sequence.RNA.__deepcopy__", "skbio.sequence.RNA.__eq__", "skbio.sequence.RNA.__ge__", "skbio.sequence.RNA.__getitem__", "skbio.sequence.RNA.__getstate__", "skbio.sequence.RNA.__gt__", "skbio.sequence.RNA.__iter__", "skbio.sequence.RNA.__le__", "skbio.sequence.RNA.__len__", "skbio.sequence.RNA.__lt__", "skbio.sequence.RNA.__ne__", "skbio.sequence.RNA.__reversed__", "skbio.sequence.RNA.__str__", "skbio.sequence.RNA.complement", "skbio.sequence.RNA.concat", "skbio.sequence.RNA.count", "skbio.sequence.RNA.definites", "skbio.sequence.RNA.degap", "skbio.sequence.RNA.degenerates", "skbio.sequence.RNA.distance", "skbio.sequence.RNA.expand_degenerates", "skbio.sequence.RNA.find_motifs", "skbio.sequence.RNA.find_with_regex", "skbio.sequence.RNA.frequencies", "skbio.sequence.RNA.gaps", "skbio.sequence.RNA.gc_content", "skbio.sequence.RNA.gc_frequency", "skbio.sequence.RNA.has_definites", "skbio.sequence.RNA.has_degenerates", "skbio.sequence.RNA.has_gaps", "skbio.sequence.RNA.has_interval_metadata", "skbio.sequence.RNA.has_metadata", "skbio.sequence.RNA.has_nondegenerates", "skbio.sequence.RNA.has_positional_metadata", "skbio.sequence.RNA.index", "skbio.sequence.RNA.is_reverse_complement", "skbio.sequence.RNA.iter_contiguous", "skbio.sequence.RNA.iter_kmers", "skbio.sequence.RNA.kmer_frequencies", "skbio.sequence.RNA.lowercase", "skbio.sequence.RNA.match_frequency", "skbio.sequence.RNA.matches", "skbio.sequence.RNA.mismatch_frequency", "skbio.sequence.RNA.mismatches", "skbio.sequence.RNA.nondegenerates", "skbio.sequence.RNA.read", "skbio.sequence.RNA.replace", "skbio.sequence.RNA.reverse_complement", "skbio.sequence.RNA.reverse_transcribe", "skbio.sequence.RNA.to_definites", "skbio.sequence.RNA.to_indices", "skbio.sequence.RNA.to_regex", "skbio.sequence.RNA.translate", "skbio.sequence.RNA.translate_six_frames", "skbio.sequence.RNA.write", "skbio.sequence.Sequence", "skbio.sequence.Sequence.__bool__", "skbio.sequence.Sequence.__contains__", "skbio.sequence.Sequence.__copy__", "skbio.sequence.Sequence.__deepcopy__", "skbio.sequence.Sequence.__eq__", "skbio.sequence.Sequence.__ge__", "skbio.sequence.Sequence.__getitem__", "skbio.sequence.Sequence.__getstate__", "skbio.sequence.Sequence.__gt__", "skbio.sequence.Sequence.__iter__", "skbio.sequence.Sequence.__le__", "skbio.sequence.Sequence.__len__", "skbio.sequence.Sequence.__lt__", "skbio.sequence.Sequence.__ne__", "skbio.sequence.Sequence.__reversed__", "skbio.sequence.Sequence.__str__", "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.has_interval_metadata", "skbio.sequence.Sequence.has_metadata", "skbio.sequence.Sequence.has_positional_metadata", "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.__contains__", "skbio.sequence.SubstitutionMatrix.__eq__", "skbio.sequence.SubstitutionMatrix.__ge__", "skbio.sequence.SubstitutionMatrix.__getitem__", "skbio.sequence.SubstitutionMatrix.__getstate__", "skbio.sequence.SubstitutionMatrix.__gt__", "skbio.sequence.SubstitutionMatrix.__le__", "skbio.sequence.SubstitutionMatrix.__lt__", "skbio.sequence.SubstitutionMatrix.__ne__", "skbio.sequence.SubstitutionMatrix.__str__", "skbio.sequence.SubstitutionMatrix.between", "skbio.sequence.SubstitutionMatrix.by_name", "skbio.sequence.SubstitutionMatrix.copy", "skbio.sequence.SubstitutionMatrix.filter", "skbio.sequence.SubstitutionMatrix.from_dict", "skbio.sequence.SubstitutionMatrix.from_iterable", "skbio.sequence.SubstitutionMatrix.get_names", "skbio.sequence.SubstitutionMatrix.identity", "skbio.sequence.SubstitutionMatrix.index", "skbio.sequence.SubstitutionMatrix.plot", "skbio.sequence.SubstitutionMatrix.read", "skbio.sequence.SubstitutionMatrix.redundant_form", "skbio.sequence.SubstitutionMatrix.to_data_frame", "skbio.sequence.SubstitutionMatrix.to_dict", "skbio.sequence.SubstitutionMatrix.transpose", "skbio.sequence.SubstitutionMatrix.within", "skbio.sequence.SubstitutionMatrix.write", "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 matrices and distance-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.__contains__", "skbio.stats.distance.DissimilarityMatrix.__eq__", "skbio.stats.distance.DissimilarityMatrix.__ge__", "skbio.stats.distance.DissimilarityMatrix.__getitem__", "skbio.stats.distance.DissimilarityMatrix.__getstate__", "skbio.stats.distance.DissimilarityMatrix.__gt__", "skbio.stats.distance.DissimilarityMatrix.__le__", "skbio.stats.distance.DissimilarityMatrix.__lt__", "skbio.stats.distance.DissimilarityMatrix.__ne__", "skbio.stats.distance.DissimilarityMatrix.__str__", "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.to_data_frame", "skbio.stats.distance.DissimilarityMatrix.transpose", "skbio.stats.distance.DissimilarityMatrix.within", "skbio.stats.distance.DissimilarityMatrix.write", "skbio.stats.distance.DissimilarityMatrixError", "skbio.stats.distance.DistanceMatrix", "skbio.stats.distance.DistanceMatrix.__contains__", "skbio.stats.distance.DistanceMatrix.__eq__", "skbio.stats.distance.DistanceMatrix.__ge__", "skbio.stats.distance.DistanceMatrix.__getitem__", "skbio.stats.distance.DistanceMatrix.__getstate__", "skbio.stats.distance.DistanceMatrix.__gt__", "skbio.stats.distance.DistanceMatrix.__le__", "skbio.stats.distance.DistanceMatrix.__lt__", "skbio.stats.distance.DistanceMatrix.__ne__", "skbio.stats.distance.DistanceMatrix.__str__", "skbio.stats.distance.DistanceMatrix.between", "skbio.stats.distance.DistanceMatrix.condensed_form", "skbio.stats.distance.DistanceMatrix.copy", "skbio.stats.distance.DistanceMatrix.filter", "skbio.stats.distance.DistanceMatrix.from_iterable", "skbio.stats.distance.DistanceMatrix.index", "skbio.stats.distance.DistanceMatrix.permute", "skbio.stats.distance.DistanceMatrix.plot", "skbio.stats.distance.DistanceMatrix.read", "skbio.stats.distance.DistanceMatrix.redundant_form", "skbio.stats.distance.DistanceMatrix.to_data_frame", "skbio.stats.distance.DistanceMatrix.to_series", "skbio.stats.distance.DistanceMatrix.transpose", "skbio.stats.distance.DistanceMatrix.within", "skbio.stats.distance.DistanceMatrix.write", "skbio.stats.distance.DistanceMatrixError", "skbio.stats.distance.MissingIDError", "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.AverageGradientANOVA.__eq__", "skbio.stats.gradient.AverageGradientANOVA.__ge__", "skbio.stats.gradient.AverageGradientANOVA.__getstate__", "skbio.stats.gradient.AverageGradientANOVA.__gt__", "skbio.stats.gradient.AverageGradientANOVA.__hash__", "skbio.stats.gradient.AverageGradientANOVA.__le__", "skbio.stats.gradient.AverageGradientANOVA.__lt__", "skbio.stats.gradient.AverageGradientANOVA.__ne__", "skbio.stats.gradient.AverageGradientANOVA.__str__", "skbio.stats.gradient.AverageGradientANOVA.get_trajectories", "skbio.stats.gradient.CategoryResults", "skbio.stats.gradient.CategoryResults.__eq__", "skbio.stats.gradient.CategoryResults.__ge__", "skbio.stats.gradient.CategoryResults.__getstate__", "skbio.stats.gradient.CategoryResults.__gt__", "skbio.stats.gradient.CategoryResults.__hash__", "skbio.stats.gradient.CategoryResults.__le__", "skbio.stats.gradient.CategoryResults.__lt__", "skbio.stats.gradient.CategoryResults.__ne__", "skbio.stats.gradient.CategoryResults.__str__", "skbio.stats.gradient.CategoryResults.to_files", "skbio.stats.gradient.FirstDifferenceGradientANOVA", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__eq__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__ge__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__getstate__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__gt__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__hash__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__le__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__lt__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__ne__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__str__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.get_trajectories", "skbio.stats.gradient.GradientANOVA", "skbio.stats.gradient.GradientANOVA.__eq__", "skbio.stats.gradient.GradientANOVA.__ge__", "skbio.stats.gradient.GradientANOVA.__getstate__", "skbio.stats.gradient.GradientANOVA.__gt__", "skbio.stats.gradient.GradientANOVA.__hash__", "skbio.stats.gradient.GradientANOVA.__le__", "skbio.stats.gradient.GradientANOVA.__lt__", "skbio.stats.gradient.GradientANOVA.__ne__", "skbio.stats.gradient.GradientANOVA.__str__", 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239, 261, 273, 275, 341, 394, 397, 414, 436, 448, 451, 492, 494, 506, 881], "The": [0, 1, 16, 17, 45, 46, 47, 48, 49, 51, 52, 54, 55, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 72, 73, 78, 79, 80, 81, 83, 88, 90, 94, 95, 96, 97, 99, 102, 103, 105, 106, 107, 108, 109, 110, 111, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150, 160, 161, 162, 173, 175, 176, 177, 178, 179, 180, 181, 182, 183, 186, 187, 188, 190, 191, 193, 194, 203, 204, 205, 214, 215, 216, 217, 218, 219, 221, 224, 227, 229, 234, 239, 240, 241, 243, 245, 249, 257, 259, 260, 262, 263, 264, 271, 273, 275, 279, 280, 281, 290, 291, 292, 295, 298, 300, 305, 310, 311, 313, 315, 319, 325, 327, 328, 329, 330, 331, 338, 341, 343, 346, 349, 351, 356, 361, 362, 364, 366, 370, 376, 378, 380, 381, 382, 383, 390, 394, 396, 397, 399, 402, 404, 409, 414, 415, 416, 418, 420, 424, 432, 434, 435, 437, 438, 439, 446, 448, 451, 454, 455, 456, 458, 461, 463, 468, 473, 474, 475, 477, 479, 480, 481, 482, 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78, 94, 105, 106, 110, 111, 134, 135, 136, 137, 140, 141, 142, 143, 145, 146, 219, 221, 229, 238, 243, 251, 252, 262, 271, 275, 277, 278, 279, 280, 291, 292, 300, 309, 313, 329, 338, 341, 343, 351, 360, 364, 381, 390, 394, 396, 397, 404, 413, 418, 426, 427, 437, 446, 449, 451, 453, 454, 455, 463, 472, 482, 490, 492, 493, 494, 504, 506, 515, 521, 528, 546, 557, 564, 569, 581, 586, 590, 593, 596, 599, 600, 602, 603, 604, 608, 698, 708, 709, 710, 711, 713, 718, 719, 723, 727, 749, 750, 752, 781, 783, 784, 787, 788, 789, 791, 804, 806, 807, 812, 875, 877, 878, 879, 880], "gene": [1, 139, 193, 203, 215, 218, 222, 456, 533, 539, 545], "metabolit": [1, 727], "purpos": [1, 66, 69, 145, 147, 281, 723, 874, 881], "singl": [1, 28, 45, 48, 56, 78, 84, 85, 93, 105, 106, 108, 135, 136, 137, 138, 141, 143, 144, 145, 146, 193, 203, 215, 229, 232, 237, 249, 262, 276, 300, 303, 308, 319, 329, 342, 351, 354, 359, 370, 381, 395, 404, 407, 412, 424, 437, 452, 463, 466, 471, 477, 482, 494, 528, 543, 607, 724, 755, 863, 875, 879, 881], "what": [1, 78, 94, 103, 105, 106, 107, 141, 145, 148, 150, 178, 179, 183, 188, 218, 262, 329, 381, 437, 482, 607, 697, 726, 879, 881], "vari": [1, 603, 723, 725, 726], "wide": [1, 54, 94, 240, 310, 361, 415, 473], "For": [1, 28, 47, 55, 59, 66, 94, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 148, 203, 218, 219, 220, 221, 222, 271, 280, 338, 343, 344, 390, 396, 397, 446, 455, 456, 490, 493, 506, 515, 521, 528, 533, 564, 569, 590, 596, 599, 600, 601, 602, 603, 605, 607, 609, 675, 709, 710, 711, 712, 713, 723, 725, 726, 727, 754, 791, 812, 813, 815, 816, 875, 877, 879], "microbiom": [1, 94, 108, 528, 533, 718], "survei": 1, "could": [1, 28, 85, 136, 137, 144, 148, 181, 183, 186, 188, 528, 533, 547, 599, 601, 602, 603, 604, 607, 709, 725, 780, 782, 815, 816, 875], "all": [1, 16, 28, 29, 46, 47, 51, 52, 54, 60, 61, 62, 67, 69, 78, 79, 80, 90, 94, 95, 99, 102, 103, 105, 106, 107, 108, 131, 132, 134, 135, 136, 137, 138, 139, 140, 142, 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773, 774, 803, 805, 806, 813, 877], "given": [1, 55, 59, 69, 80, 83, 88, 90, 99, 103, 107, 108, 111, 136, 137, 141, 142, 145, 160, 162, 178, 179, 181, 182, 186, 187, 216, 219, 221, 271, 275, 280, 338, 341, 343, 390, 394, 396, 446, 451, 455, 490, 492, 493, 510, 515, 521, 543, 561, 564, 569, 586, 590, 596, 600, 601, 604, 710, 711, 713, 717, 722, 724, 726, 734, 769, 791, 812, 839, 840, 852, 881], "number": [1, 28, 40, 45, 48, 69, 70, 71, 72, 75, 76, 77, 78, 79, 81, 82, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 99, 100, 101, 102, 105, 106, 107, 131, 132, 134, 135, 136, 138, 141, 143, 144, 146, 147, 190, 193, 203, 214, 234, 241, 249, 266, 268, 305, 311, 319, 333, 335, 356, 362, 370, 385, 387, 409, 416, 424, 441, 443, 468, 474, 477, 486, 488, 494, 509, 527, 528, 533, 537, 538, 540, 541, 542, 543, 547, 571, 599, 600, 601, 602, 603, 604, 605, 607, 642, 686, 697, 713, 717, 718, 720, 721, 723, 724, 726, 727, 728, 754, 761, 798, 817, 818], "observ": [1, 78, 81, 90, 93, 101, 105, 106, 111, 222, 249, 275, 293, 319, 341, 344, 370, 394, 397, 424, 451, 456, 477, 492, 528, 607, 698, 723, 726, 727, 785, 813, 881], "particular": [1, 734, 816, 881], "associ": [1, 35, 69, 94, 137, 145, 146, 147, 150, 175, 176, 177, 193, 214, 216, 218, 222, 344, 397, 456, 600, 607, 697, 717, 721, 724, 725, 726, 764, 770, 803, 875], "throughout": [1, 140, 281, 290, 726, 880], "array_lik": [1, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 107, 108, 111, 229, 247, 248, 262, 272, 300, 317, 318, 329, 339, 351, 368, 369, 381, 391, 404, 422, 423, 437, 447, 463, 476, 482, 491, 526, 527, 529, 530, 531, 532, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 545, 547, 599, 601, 602, 603, 604, 607, 714, 717, 721, 724, 727, 728], "anyth": [1, 136, 137, 144, 148, 456, 840, 851, 863, 881], "convert": [1, 132, 134, 135, 136, 138, 141, 143, 146, 190, 222, 245, 274, 275, 315, 340, 341, 344, 366, 393, 394, 397, 420, 450, 451, 456, 475, 492, 547, 588, 600, 728, 754, 819], "d": [1, 16, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 105, 106, 107, 132, 133, 138, 141, 142, 222, 344, 397, 505, 509, 514, 520, 525, 526, 527, 528, 531, 532, 534, 535, 536, 539, 540, 541, 542, 543, 544, 545, 546, 558, 563, 568, 582, 589, 593, 595, 599, 600, 601, 602, 603, 607, 642, 664, 686, 699, 709, 717, 726, 727, 728, 735, 736, 749, 750, 752, 754, 755, 756, 757, 758, 760, 761, 763, 764, 765, 767, 768, 769, 770, 774, 780, 781, 782, 783, 784, 790, 794, 795, 796, 798, 799, 800, 801, 803, 804, 805, 808, 809, 810, 811, 813, 814, 875, 877, 879, 881], "numpi": [1, 107, 498, 516, 526, 527, 529, 530, 531, 532, 534, 535, 536, 537, 539, 540, 541, 542, 543, 545, 546, 547, 551, 565, 575, 583, 591, 599, 603, 605, 607, 608, 642, 664, 686, 697, 698, 723, 725, 726, 727, 728, 759, 798, 877], "arrai": [1, 16, 47, 50, 78, 94, 105, 106, 136, 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762, 793, 794, 805, 806, 811, 813, 814, 824, 841, 863, 875, 877, 879, 881], "row": [1, 28, 103, 107, 108, 111, 131, 143, 193, 494, 498, 513, 527, 528, 530, 533, 534, 535, 537, 538, 540, 541, 542, 543, 546, 547, 551, 562, 575, 587, 588, 593, 599, 600, 601, 602, 603, 604, 605, 607, 699, 712, 713, 716, 720, 726, 727, 817], "so": [1, 2, 47, 60, 61, 62, 63, 64, 65, 67, 78, 103, 105, 106, 107, 136, 141, 145, 148, 190, 191, 203, 206, 251, 252, 426, 427, 601, 675, 698, 712, 713, 714, 718, 720, 723, 725, 726, 727, 813, 875, 879, 881], "column": [1, 16, 28, 52, 53, 54, 107, 131, 136, 138, 139, 142, 143, 146, 147, 240, 259, 265, 310, 327, 332, 361, 378, 384, 415, 434, 440, 456, 473, 480, 485, 494, 498, 513, 517, 526, 527, 528, 533, 534, 535, 546, 551, 562, 566, 575, 587, 588, 592, 599, 600, 601, 602, 603, 604, 605, 607, 642, 686, 698, 709, 712, 713, 714, 716, 720, 721, 725, 726, 772, 776, 817, 818], "some": [1, 16, 68, 78, 80, 90, 94, 136, 138, 141, 144, 145, 160, 161, 162, 193, 217, 222, 344, 397, 527, 540, 541, 542, 713, 723, 726, 840, 879, 881], "incorpor": [1, 94, 524], "relationship": [1, 94, 141, 712, 713, 720, 723, 727, 814], "between": [1, 16, 61, 64, 74, 79, 80, 84, 95, 102, 105, 106, 107, 111, 131, 136, 137, 138, 140, 143, 146, 147, 206, 220, 240, 245, 266, 267, 268, 269, 310, 315, 333, 334, 335, 336, 361, 366, 385, 386, 387, 388, 415, 420, 441, 442, 443, 444, 473, 475, 486, 487, 488, 489, 494, 498, 510, 522, 523, 524, 528, 533, 543, 546, 547, 551, 561, 571, 575, 586, 599, 600, 601, 602, 603, 604, 606, 607, 642, 712, 713, 714, 720, 723, 726, 727, 734, 749, 757, 758, 759, 765, 774, 784, 803, 804, 814, 877, 879], "through": [1, 35, 60, 61, 62, 145, 174, 180, 185, 498, 551, 575, 718, 767, 881], "phylogenet": [1, 78, 94, 105, 106, 141, 143, 546, 607, 734, 757, 767, 814, 874, 877], "tree": [1, 78, 94, 105, 106, 141, 146, 147, 203, 544, 874, 875], "take": [1, 107, 143, 148, 160, 161, 162, 245, 272, 315, 339, 366, 391, 420, 447, 475, 491, 510, 528, 561, 571, 586, 600, 601, 675, 712, 720, 723, 724, 814, 840, 879, 881], "treenod": [1, 78, 94, 105, 106, 141, 544, 813, 814, 875, 879], "map": [1, 49, 56, 108, 150, 163, 222, 293, 344, 397, 601, 604, 607, 608, 642, 686, 709, 725, 727, 773, 776, 877], "valu": [1, 3, 4, 7, 9, 10, 11, 18, 19, 21, 23, 24, 25, 34, 37, 39, 41, 47, 51, 60, 61, 62, 63, 64, 65, 67, 69, 80, 90, 102, 103, 106, 131, 132, 133, 135, 136, 137, 138, 139, 140, 145, 146, 151, 152, 154, 156, 157, 158, 164, 165, 167, 169, 170, 171, 190, 193, 195, 197, 198, 199, 202, 207, 209, 210, 211, 214, 218, 222, 223, 228, 231, 233, 235, 239, 240, 257, 265, 272, 273, 283, 285, 286, 287, 293, 294, 299, 302, 304, 306, 310, 325, 332, 339, 344, 345, 350, 353, 355, 357, 361, 376, 384, 391, 397, 398, 403, 406, 408, 410, 414, 415, 432, 440, 447, 448, 456, 457, 462, 465, 467, 469, 473, 479, 485, 491, 497, 500, 501, 502, 505, 520, 525, 528, 530, 533, 537, 538, 539, 540, 541, 542, 545, 550, 553, 554, 555, 558, 568, 574, 577, 578, 579, 582, 595, 599, 600, 601, 602, 603, 604, 605, 607, 610, 611, 613, 615, 616, 617, 621, 622, 624, 626, 627, 628, 630, 632, 633, 635, 637, 638, 639, 642, 643, 644, 646, 648, 649, 650, 654, 655, 657, 659, 660, 661, 663, 665, 666, 668, 670, 671, 672, 674, 676, 677, 679, 681, 682, 683, 687, 688, 690, 692, 693, 694, 697, 700, 701, 703, 705, 706, 707, 709, 712, 713, 717, 718, 720, 722, 723, 724, 725, 726, 727, 734, 737, 738, 741, 744, 746, 747, 754, 756, 759, 798, 805, 816, 817, 818, 822, 823, 826, 828, 829, 830, 831, 840, 842, 843, 845, 847, 848, 849, 852, 854, 855, 857, 859, 860, 861, 863, 865, 866, 868, 870, 871, 872, 881], "tip": [1, 78, 94, 105, 106, 734, 752, 754, 756, 757, 758, 759, 761, 762, 764, 765, 767, 774, 779, 780, 781, 782, 784, 785, 787, 788, 789, 795, 796, 797, 798, 800, 801, 803, 806, 807, 808, 813, 875, 879], "optim": [1, 2, 16, 79, 103, 105, 106, 107, 603, 765, 815, 874], "time": [1, 16, 45, 48, 78, 90, 99, 105, 106, 108, 136, 137, 145, 494, 534, 535, 543, 583, 599, 600, 601, 602, 604, 608, 631, 686, 720, 723, 726, 727, 734, 798, 881], "often": [1, 78, 103, 107, 135, 136, 138, 546, 607, 713, 718, 723, 838], "faster": [1, 78, 105, 106, 108, 249, 279, 292, 319, 370, 424, 454, 477, 603, 718, 787], "repeat": [1, 137, 723, 837], "call": [1, 54, 78, 79, 84, 85, 105, 106, 134, 136, 143, 146, 148, 190, 193, 240, 248, 251, 272, 291, 310, 318, 339, 361, 369, 391, 415, 423, 426, 447, 456, 473, 476, 491, 588, 600, 601, 697, 713, 723, 750, 752, 753, 756, 767, 768, 770, 783, 784, 790, 799, 804, 811, 838, 840, 841, 851, 875, 881], "reason": [1, 79, 90, 135, 141, 726, 754], "matric": [1, 62, 65, 131, 140, 344, 494, 496, 503, 506, 511, 547, 549, 556, 573, 580, 600, 601, 604, 606, 607, 714, 718, 759], "rather": [1, 83, 141, 494, 525, 607, 814], "thu": [1, 136, 137, 141, 145, 249, 319, 370, 424, 456, 477, 498, 551, 571, 575, 599, 601, 603, 607, 718], "slow": [1, 78, 103, 105, 106, 107, 874], "possibl": [1, 16, 35, 95, 99, 136, 137, 145, 146, 217, 246, 279, 281, 292, 316, 367, 421, 454, 600, 604, 726, 759, 807, 813], "disabl": [1, 78, 103, 105, 106, 107, 881], "step": [1, 28, 45, 48, 56, 78, 103, 105, 106, 107, 143, 148, 716, 723], "pass": [1, 28, 35, 48, 55, 56, 59, 66, 103, 107, 108, 109, 110, 132, 134, 136, 138, 143, 144, 146, 160, 161, 162, 174, 180, 181, 182, 183, 185, 186, 187, 188, 190, 219, 221, 222, 245, 247, 249, 271, 272, 280, 291, 315, 317, 319, 338, 339, 343, 344, 366, 368, 370, 390, 391, 396, 397, 420, 422, 424, 446, 447, 455, 456, 475, 477, 490, 491, 493, 498, 515, 521, 551, 564, 569, 575, 586, 588, 590, 596, 601, 604, 642, 710, 711, 726, 780, 782, 791, 812, 814, 863, 879, 881], "fals": [1, 14, 15, 16, 29, 30, 31, 32, 33, 45, 46, 48, 50, 51, 52, 53, 57, 60, 61, 62, 72, 73, 78, 94, 103, 105, 106, 107, 132, 135, 136, 137, 138, 139, 141, 144, 160, 161, 162, 190, 191, 193, 203, 215, 216, 222, 223, 224, 225, 227, 229, 236, 239, 240, 242, 243, 244, 246, 249, 250, 252, 253, 254, 255, 257, 258, 259, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 272, 273, 274, 275, 276, 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56, 57, 58, 60, 61, 62, 64, 66, 69, 72, 73, 78, 79, 80, 84, 90, 94, 103, 105, 106, 107, 108, 111, 132, 136, 139, 140, 141, 142, 143, 144, 145, 146, 148, 150, 160, 161, 162, 175, 177, 181, 182, 186, 187, 190, 193, 202, 206, 219, 220, 222, 224, 229, 239, 240, 241, 243, 245, 247, 249, 252, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 271, 273, 275, 276, 291, 293, 295, 300, 310, 311, 313, 315, 317, 319, 328, 329, 330, 331, 332, 333, 334, 335, 336, 338, 341, 342, 344, 346, 351, 361, 362, 364, 366, 368, 370, 380, 381, 382, 383, 384, 385, 386, 387, 388, 390, 394, 395, 397, 399, 404, 414, 415, 416, 418, 420, 422, 424, 427, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 446, 448, 451, 452, 453, 454, 456, 458, 463, 473, 474, 475, 477, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 492, 498, 505, 506, 508, 509, 510, 513, 514, 515, 520, 523, 524, 528, 530, 533, 534, 535, 537, 538, 544, 547, 551, 558, 560, 561, 562, 563, 564, 568, 575, 582, 585, 586, 587, 588, 589, 590, 595, 599, 600, 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840, 875, 879, 881], "difficult": 1, "interpret": [1, 47, 74, 78, 103, 105, 106, 107, 131, 141, 145, 525, 712, 713, 720], "error": [1, 47, 78, 90, 94, 103, 105, 106, 107, 136, 137, 143, 145, 148, 190, 217, 275, 341, 394, 451, 492, 570, 597, 598, 599, 601, 603, 723, 727, 733, 819, 875], "messag": [1, 78, 103, 105, 106, 107, 620, 664, 819, 875], "incorrect": 1, "recommend": [1, 83, 94, 143, 146, 222, 293, 344, 397, 456, 528, 546, 709, 712, 720, 726], "user": [1, 47, 104, 112, 132, 145, 147, 148, 150, 160, 161, 162, 181, 183, 186, 188, 274, 340, 393, 450, 528, 533, 713, 718, 815, 874, 877], "care": [1, 47, 136, 138, 603], "ensur": [1, 16, 47, 78, 105, 106, 148, 222, 344, 397, 496, 530, 533, 537, 549, 571, 573, 755, 817], "data": [1, 28, 54, 78, 80, 90, 94, 103, 105, 106, 107, 108, 111, 132, 135, 137, 139, 140, 142, 144, 145, 146, 147, 190, 222, 293, 344, 397, 456, 494, 496, 498, 516, 525, 526, 527, 528, 529, 532, 533, 535, 537, 539, 543, 545, 547, 549, 551, 565, 571, 573, 575, 591, 600, 607, 608, 630, 663, 674, 697, 709, 712, 713, 717, 723, 725, 726, 727, 772, 803, 807, 814, 838, 841, 874, 875, 877, 881], "condit": [1, 84, 85, 726], "follow": [1, 51, 52, 54, 66, 73, 78, 79, 94, 105, 106, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 193, 222, 229, 257, 259, 300, 325, 327, 344, 351, 376, 378, 397, 404, 432, 434, 456, 463, 479, 480, 498, 506, 526, 527, 528, 531, 532, 534, 535, 536, 540, 542, 543, 546, 551, 575, 599, 600, 601, 603, 604, 608, 709, 712, 727, 753, 790, 841, 879, 881], "confid": [1, 68, 73, 77, 84, 533, 723, 724, 734, 754], "met": [1, 344, 863], "safe": [1, 78, 103, 105, 106, 107, 145, 718, 728, 752], "cast": [1, 141, 240, 310, 361, 415, 473, 546, 547, 605, 709], "integ": [1, 16, 103, 107, 131, 132, 136, 137, 140, 141, 142, 143, 144, 229, 300, 351, 404, 463, 528, 533, 546, 547, 599, 602, 603, 604, 605, 686, 728], "neg": [1, 16, 61, 64, 67, 80, 145, 291, 530, 537, 538, 571, 712, 713, 718, 723, 727, 814], "dimension": [1, 516, 527, 540, 541, 542, 547, 565, 583, 591, 712, 719, 720, 726, 727], "equal": [1, 33, 42, 47, 67, 69, 101, 105, 106, 107, 136, 194, 200, 206, 212, 227, 236, 282, 288, 298, 307, 349, 358, 402, 411, 456, 461, 470, 494, 496, 503, 523, 540, 549, 556, 573, 580, 599, 601, 602, 603, 605, 607, 697, 712, 717, 718, 721, 726, 727, 728, 757, 813, 817, 818], "being": [1, 16, 45, 47, 48, 60, 61, 62, 78, 103, 107, 136, 137, 143, 147, 543, 603, 607, 697, 726, 735, 736, 756, 760, 763, 796, 875, 877], "confirm": [1, 119, 599, 603, 727], "uniqu": [1, 54, 58, 132, 136, 140, 141, 145, 146, 147, 275, 341, 394, 451, 492, 524, 546, 603, 709, 753, 762, 767], "root": [1, 78, 89, 94, 105, 106, 141, 147, 544, 735, 736, 749, 750, 751, 752, 754, 755, 756, 760, 763, 764, 765, 766, 769, 770, 772, 774, 778, 780, 782, 783, 790, 795, 796, 799, 801, 803, 805, 806, 808, 810, 811, 813, 814, 879], "ha": [1, 16, 28, 46, 51, 52, 60, 61, 62, 67, 111, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 182, 187, 190, 222, 239, 240, 243, 246, 256, 257, 258, 259, 270, 273, 277, 278, 279, 281, 291, 292, 293, 310, 313, 316, 324, 325, 326, 327, 337, 344, 361, 364, 367, 375, 376, 377, 378, 389, 397, 414, 415, 418, 421, 431, 432, 433, 434, 445, 448, 449, 453, 454, 456, 473, 478, 479, 480, 528, 530, 546, 697, 712, 714, 725, 726, 727, 755, 775, 778, 779, 793, 797, 813, 840, 877, 879], "node": [1, 78, 105, 106, 544, 729, 730, 734, 735, 736, 739, 743, 749, 750, 751, 753, 754, 755, 756, 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 772, 774, 775, 776, 778, 779, 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 792, 793, 795, 796, 799, 800, 803, 804, 805, 806, 807, 808, 809, 813, 875, 879], "except": [1, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 136, 141, 142, 143, 145, 149, 161, 184, 291, 508, 560, 570, 585, 597, 598, 602, 713, 729, 730, 731, 732, 733, 762, 813, 815, 816, 851, 874, 880], "branch": [1, 78, 94, 106, 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497, 500, 501, 502, 503, 505, 507, 519, 520, 549, 550, 553, 554, 555, 556, 558, 559, 567, 568, 573, 574, 577, 578, 579, 580, 582, 584, 594, 595, 610, 611, 613, 614, 615, 616, 617, 618, 621, 622, 624, 625, 626, 627, 628, 629, 632, 633, 635, 636, 637, 638, 639, 640, 643, 644, 646, 647, 648, 649, 650, 651, 654, 655, 657, 658, 659, 660, 661, 662, 665, 666, 668, 669, 670, 671, 672, 673, 676, 677, 679, 680, 681, 682, 683, 684, 687, 688, 690, 691, 692, 693, 694, 695, 700, 701, 703, 704, 705, 706, 707, 735, 736, 737, 738, 741, 742, 744, 746, 747, 748, 749, 750, 751, 753, 754, 757, 758, 759, 760, 763, 764, 765, 766, 783, 784, 785, 786, 792, 793, 794, 799, 800, 801, 804, 805, 806, 807, 808, 810, 811, 822, 823, 826, 827, 828, 829, 830, 833, 840, 841, 842, 843, 845, 846, 847, 848, 849, 850, 851, 854, 855, 857, 858, 859, 860, 861, 862, 865, 866, 868, 869, 870, 871, 872, 873, 879, 881], "kei": [5, 28, 45, 48, 49, 51, 56, 67, 135, 136, 138, 146, 214, 218, 222, 246, 257, 265, 272, 316, 325, 332, 339, 344, 367, 376, 384, 391, 397, 421, 432, 440, 447, 456, 479, 485, 491, 510, 561, 586, 785, 805, 813, 881], "helper": [6, 20, 36, 153, 166, 196, 208, 230, 284, 301, 352, 405, 464, 499, 552, 576, 612, 623, 634, 645, 656, 667, 678, 689, 702, 740, 817, 818, 825, 844, 856, 867, 879], "pickl": [6, 20, 36, 153, 166, 196, 208, 230, 284, 301, 352, 405, 464, 499, 552, 576, 612, 623, 634, 645, 656, 667, 678, 689, 702, 740, 825, 844, 856, 867], "hash": [8, 22, 155, 168, 614, 625, 636, 647, 658, 669, 680, 691, 704, 742, 827, 846, 858, 869], "str": [13, 17, 27, 33, 38, 43, 55, 59, 67, 103, 107, 108, 109, 110, 111, 132, 138, 139, 146, 150, 159, 172, 175, 176, 177, 181, 182, 183, 186, 187, 188, 190, 201, 213, 219, 221, 222, 224, 232, 237, 238, 241, 245, 246, 247, 248, 249, 260, 261, 263, 265, 266, 267, 268, 269, 271, 272, 274, 275, 280, 281, 289, 295, 303, 308, 309, 311, 315, 316, 317, 318, 319, 328, 330, 332, 333, 334, 335, 336, 338, 339, 340, 341, 343, 344, 346, 354, 359, 360, 362, 366, 367, 368, 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758, 761, 775, 777, 778, 779, 781, 784, 787, 788, 789, 792, 804, 806, 807, 814, 818, 840], "whether": [14, 29, 30, 33, 42, 51, 52, 72, 73, 94, 139, 148, 160, 162, 190, 224, 227, 236, 253, 254, 255, 256, 257, 258, 259, 262, 263, 264, 282, 288, 295, 298, 307, 321, 322, 323, 324, 325, 326, 327, 329, 330, 331, 346, 349, 358, 372, 373, 374, 375, 376, 377, 378, 379, 381, 382, 383, 399, 402, 411, 428, 429, 430, 431, 432, 433, 434, 437, 438, 439, 458, 461, 470, 478, 479, 480, 482, 483, 484, 494, 503, 524, 528, 539, 545, 556, 580, 599, 601, 602, 603, 708, 720, 721], "is_zero_bas": 15, "set": [15, 16, 46, 49, 53, 54, 78, 94, 105, 106, 111, 136, 138, 140, 143, 150, 190, 203, 216, 222, 240, 249, 262, 265, 275, 293, 310, 319, 329, 332, 341, 344, 361, 370, 381, 384, 394, 397, 415, 424, 437, 440, 451, 456, 473, 477, 482, 485, 492, 506, 514, 520, 525, 537, 563, 568, 589, 595, 607, 697, 718, 720, 723, 725, 726, 727, 735, 736, 751, 753, 756, 760, 763, 764, 766, 786, 800, 801, 813, 820, 831, 832, 837, 877, 881], "alig": 15, "stripe": [16, 66], "band": 16, "must": [16, 28, 45, 48, 54, 55, 59, 78, 80, 94, 105, 106, 107, 108, 111, 132, 134, 136, 137, 140, 141, 142, 143, 145, 146, 161, 218, 219, 221, 222, 240, 245, 265, 271, 278, 280, 310, 315, 332, 338, 343, 344, 361, 366, 384, 390, 396, 397, 415, 420, 440, 446, 453, 455, 456, 473, 475, 485, 490, 493, 508, 515, 521, 528, 533, 544, 547, 560, 564, 569, 585, 590, 596, 599, 600, 601, 602, 603, 605, 607, 630, 663, 674, 697, 709, 710, 711, 712, 717, 726, 727, 728, 756, 791, 798, 806, 812, 813, 814, 817, 819, 839, 840, 863, 881], "instanti": [16, 135, 148, 293, 881], "callabl": [16, 28, 45, 48, 56, 103, 107, 108, 111, 510, 528, 561, 586], "reus": [16, 722], "larg": [16, 79, 83, 105, 106, 131, 136, 143, 537, 538, 600, 720, 726, 752, 759], "collect": [16, 95, 99, 101, 190, 505, 543, 558, 582, 697], "upper": [16, 83, 84, 136, 143, 193, 203, 215, 217, 586, 593, 601], "lowercas": [16, 135, 136, 137, 138, 144, 222, 240, 293, 310, 344, 361, 397, 415, 456, 473], "q": [16, 83, 133, 344, 713, 714], "h": [16, 69, 70, 74, 82, 94, 95, 96, 97, 98, 99, 136, 143, 146, 191, 222, 344, 397, 755, 756, 761, 764, 795, 796, 797, 800, 801, 810, 811, 813, 879], "l": [16, 70, 71, 78, 83, 84, 94, 102, 135, 137, 147, 291, 344, 543, 601, 698, 712, 713, 720, 806], "k": [16, 69, 74, 94, 95, 97, 98, 99, 108, 222, 249, 263, 264, 319, 330, 331, 344, 370, 382, 383, 397, 424, 438, 439, 477, 483, 484, 494, 506, 524, 543, 600, 607, 764, 798, 805, 813], "m": [16, 63, 69, 78, 94, 105, 106, 132, 133, 135, 137, 143, 147, 222, 281, 282, 291, 344, 397, 506, 600, 603, 607, 709, 712, 713, 719, 720, 722, 725, 797, 814], "w": [16, 47, 69, 70, 77, 90, 94, 102, 132, 133, 134, 190, 222, 344, 397, 528, 543], "y": [16, 69, 80, 137, 144, 222, 344, 397, 536, 540, 541, 545, 601, 604, 607, 698, 709, 713, 714, 719, 720, 725, 759, 805], "v": [16, 105, 106, 222, 227, 236, 298, 307, 344, 349, 358, 397, 402, 411, 461, 470, 525, 539, 543, 545, 725, 726, 805], "z": [16, 54, 77, 145, 344, 604, 709, 759, 805], "x": [16, 80, 96, 137, 144, 275, 293, 341, 344, 394, 451, 492, 525, 526, 527, 529, 530, 531, 532, 534, 535, 536, 537, 540, 541, 542, 543, 545, 601, 604, 607, 698, 699, 709, 712, 713, 714, 720, 723, 726, 727, 759, 769, 790, 793, 805, 809, 814, 839, 881], "gap_open_penalti": [16, 60, 61, 62, 63, 64, 65], "int": [16, 40, 50, 57, 60, 61, 62, 63, 64, 65, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 107, 108, 111, 132, 138, 139, 144, 161, 190, 193, 203, 214, 218, 229, 234, 241, 247, 248, 252, 260, 262, 263, 264, 266, 268, 272, 290, 300, 305, 311, 317, 318, 328, 329, 330, 331, 333, 335, 339, 351, 356, 362, 368, 369, 380, 381, 382, 383, 385, 387, 391, 404, 409, 416, 422, 423, 427, 435, 437, 438, 439, 441, 443, 447, 453, 454, 463, 468, 474, 476, 481, 482, 483, 484, 486, 488, 491, 512, 513, 524, 526, 527, 533, 539, 545, 562, 587, 599, 601, 602, 603, 604, 605, 607, 642, 686, 697, 709, 713, 717, 718, 720, 721, 724, 726, 727, 728, 734, 755, 759, 761, 770, 776, 785, 786, 798, 813, 818, 819, 839, 852], "option": [16, 28, 45, 47, 48, 50, 53, 54, 55, 56, 57, 59, 60, 61, 62, 64, 65, 66, 67, 69, 72, 73, 78, 83, 84, 85, 90, 94, 97, 103, 105, 106, 107, 108, 111, 134, 136, 137, 142, 143, 145, 146, 147, 150, 160, 161, 162, 181, 182, 183, 186, 187, 188, 190, 193, 203, 214, 218, 219, 220, 221, 222, 227, 239, 240, 241, 245, 247, 248, 249, 252, 260, 262, 263, 264, 266, 268, 271, 274, 275, 280, 281, 290, 291, 292, 298, 310, 311, 315, 317, 318, 319, 328, 329, 330, 331, 333, 335, 338, 340, 341, 343, 344, 349, 361, 362, 366, 368, 369, 370, 380, 381, 382, 383, 385, 387, 390, 393, 394, 396, 397, 402, 414, 415, 416, 420, 422, 423, 424, 427, 435, 437, 438, 439, 441, 443, 446, 450, 451, 453, 454, 455, 456, 461, 473, 474, 475, 476, 477, 481, 482, 483, 484, 486, 488, 490, 492, 493, 505, 508, 510, 514, 515, 521, 524, 528, 533, 534, 535, 537, 538, 547, 558, 560, 561, 563, 564, 569, 582, 585, 586, 588, 589, 590, 596, 599, 600, 601, 602, 603, 604, 605, 607, 642, 697, 709, 710, 711, 713, 714, 717, 718, 720, 721, 724, 725, 726, 727, 728, 734, 755, 772, 777, 791, 798, 805, 806, 812, 813, 814, 817, 818, 839, 840, 841, 863, 877, 881], "cannot": [16, 28, 45, 48, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 136, 137, 140, 141, 145, 181, 182, 186, 187, 190, 240, 293, 310, 361, 415, 473, 528, 599, 600, 601, 602, 603, 697, 709, 725, 727, 728, 767, 770, 798, 875], "gap_extend_penalti": [16, 60, 61, 62, 63, 64, 65], "score_s": 16, "your": [16, 54, 78, 103, 105, 106, 107, 137, 145, 148, 203, 603, 723, 726, 875, 879, 881], "estim": [16, 69, 72, 73, 77, 79, 81, 83, 84, 85, 90, 96, 533, 717, 725, 726, 727], "best": [16, 60, 61, 62, 63, 64, 65, 84, 85, 525, 600, 712, 816], "255": [16, 713], "mask_length": 16, "suggest": [16, 161, 181, 182, 186, 187, 726], "len": [16, 28, 40, 234, 305, 356, 409, 468, 506, 605, 727, 735, 736, 760, 763, 801, 813, 881], "special": [16, 140, 148], "concern": [16, 140], "detail": [16, 53, 54, 66, 67, 94, 108, 110, 111, 135, 136, 137, 138, 139, 143, 144, 146, 147, 148, 292, 456, 498, 551, 575, 600, 604, 709, 712, 713, 720, 814, 875], "descript": [16, 69, 78, 83, 88, 89, 99, 103, 105, 106, 107, 131, 132, 136, 137, 138, 139, 141, 143, 145, 147, 498, 551, 575, 757, 813, 877, 879], "after": [16, 45, 48, 60, 61, 62, 136, 137, 145, 146, 147, 148, 206, 217, 533, 539, 540, 600, 601, 604, 607, 712, 727, 788, 790, 807], "locat": [16, 55, 59, 135, 141, 146, 175, 176, 177, 193, 219, 221, 247, 248, 271, 280, 317, 318, 338, 343, 368, 369, 390, 396, 422, 423, 446, 455, 476, 490, 493, 515, 521, 564, 569, 590, 596, 710, 711, 791, 795, 812, 817, 880], "heurist": [16, 603, 718], "found": [16, 101, 133, 135, 136, 137, 138, 141, 143, 146, 181, 183, 186, 188, 275, 341, 394, 451, 492, 508, 560, 585, 600, 601, 603, 727, 757, 767, 768, 769, 770, 780, 782, 798, 813], "check": [16, 137, 161, 181, 186, 194, 203, 206, 217, 495, 496, 534, 535, 546, 547, 548, 549, 571, 572, 573, 608, 712, 713, 726, 817, 818, 838, 881], "largest": [16, 102], "maxim": [16, 94, 600, 713], "sw": [16, 725], "avoid": [16, 145, 146, 148, 217, 698, 721, 810, 811], "pick": [16, 726], "belong": [16, 70, 74, 139, 528, 533, 599, 602, 603], "share": [16, 51, 52, 54, 69, 240, 257, 259, 310, 325, 327, 361, 376, 378, 415, 432, 434, 456, 473, 479, 480, 879], "partial": [16, 94, 217], "librari": [16, 66, 105, 106, 136, 874, 875], "mask": [16, 275, 341, 394, 451, 492, 539, 545], "loci": 16, "nearbi": 16, "unmask": 16, "element": [16, 140, 190, 494, 498, 510, 530, 534, 535, 547, 551, 561, 571, 575, 586, 686, 709, 712, 716, 717, 721, 724, 726, 727, 728, 837], "15": [16, 62, 65, 83, 133, 142, 145, 608, 723, 726, 727, 803], "mask_auto": 16, "automat": [16, 45, 48, 54, 55, 59, 140, 144, 145, 174, 185, 193, 219, 221, 265, 271, 280, 332, 338, 343, 384, 390, 396, 440, 446, 455, 485, 490, 493, 515, 521, 546, 564, 569, 590, 596, 699, 710, 711, 759, 791, 812, 875], "max": [16, 69, 70, 90, 726, 727, 774], "score_onli": 16, "prevent": 16, "babp": 16, "overrid": [16, 61, 64, 94, 150, 160, 161, 162, 181, 186, 790, 881], "score_filt": 16, "distance_filt": 16, "override_skip_babp": 16, "highest": [16, 141], "preced": [16, 134, 141, 143], "less": [16, 69, 78, 85, 105, 106, 108, 143, 145, 263, 264, 330, 331, 382, 383, 438, 439, 483, 484, 524, 601, 604, 697, 712, 728, 785, 819], "save": [16, 203, 547, 630, 663, 674, 787], "computation": 16, "filter": [16, 47, 66, 144, 243, 313, 364, 418, 604, 806, 881], "overridden": [16, 28, 138, 814], "regardless": [16, 46, 53, 54, 146, 291, 512, 605], "argument": [16, 28, 55, 56, 59, 66, 140, 160, 161, 162, 174, 181, 182, 183, 185, 186, 187, 188, 219, 221, 265, 271, 278, 279, 280, 332, 338, 343, 384, 390, 396, 440, 446, 453, 454, 455, 485, 490, 493, 494, 510, 515, 521, 526, 561, 564, 569, 586, 590, 596, 605, 710, 711, 791, 812, 840, 863], "caus": [16, 145, 190, 291], "calcul": [16, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 105, 106, 108, 111, 131, 251, 252, 426, 427, 528, 533, 536, 544, 545, 599, 600, 601, 602, 603, 607, 631, 642, 686, 717, 721, 724, 726, 727, 757, 764, 803, 874, 877], "none": [16, 28, 45, 47, 48, 55, 56, 57, 61, 62, 64, 65, 66, 78, 90, 94, 103, 105, 106, 107, 108, 132, 136, 140, 148, 150, 160, 162, 175, 176, 177, 181, 186, 190, 193, 203, 214, 216, 218, 219, 222, 241, 245, 247, 248, 249, 260, 271, 275, 276, 293, 311, 315, 317, 318, 319, 328, 338, 341, 342, 344, 362, 366, 368, 369, 370, 380, 390, 394, 395, 397, 416, 420, 422, 423, 424, 435, 446, 451, 452, 456, 474, 475, 476, 477, 481, 490, 492, 510, 514, 515, 528, 533, 534, 535, 537, 538, 539, 547, 561, 563, 564, 571, 586, 589, 590, 599, 600, 601, 602, 603, 604, 605, 609, 631, 642, 675, 697, 699, 709, 710, 714, 717, 718, 721, 722, 724, 725, 726, 727, 734, 754, 755, 759, 762, 764, 772, 781, 783, 786, 787, 788, 789, 791, 798, 802, 803, 805, 806, 807, 810, 811, 813, 814, 840, 841, 863, 877, 879, 881], "effect": [16, 66, 76, 105, 106, 145, 190, 275, 341, 394, 451, 492, 505, 558, 582, 723, 725, 726, 727], "unless": [16, 28, 53, 72, 144, 841], "substitution_matrix": [16, 60, 61, 62, 63, 64, 65], "suppli": [16, 132, 136, 144, 181, 186, 245, 315, 366, 420, 475, 522, 727, 764], "match_scor": [16, 61, 64, 67], "ad": [16, 60, 61, 62, 63, 64, 65, 136, 146, 214, 456, 528, 533, 713, 716, 840, 879], "occur": [16, 133, 136, 137, 140, 141, 182, 187, 190, 260, 328, 380, 435, 456, 481, 727, 758, 767], "ignor": [16, 47, 69, 78, 105, 106, 133, 134, 135, 136, 137, 140, 141, 145, 148, 247, 248, 291, 292, 317, 318, 368, 369, 422, 423, 476, 508, 560, 585, 599, 600, 601, 602, 603, 718, 725, 726, 764, 783, 818, 840, 841, 877, 879, 881], "mismatch_scor": [16, 61, 64, 67], "subtract": [16, 686], "2d": [16, 60, 61, 62, 63, 64, 65, 103, 107, 108, 111, 494, 509, 518, 536, 605, 714, 721], "dict": [16, 28, 49, 55, 56, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 135, 138, 161, 181, 182, 183, 186, 187, 188, 193, 214, 218, 219, 221, 222, 249, 264, 271, 278, 279, 280, 293, 319, 331, 338, 343, 344, 370, 383, 390, 396, 397, 424, 439, 446, 453, 454, 455, 456, 477, 484, 490, 493, 494, 509, 515, 518, 521, 564, 569, 590, 596, 601, 604, 664, 710, 711, 772, 776, 785, 791, 805, 812, 840, 877, 881], "substitut": [16, 60, 61, 62, 63, 64, 65, 67, 140, 275, 341, 344, 394, 451, 492, 494, 506, 509, 511, 512, 518, 525, 816], "entir": [16, 28, 74, 222, 293, 344, 397, 456], "combin": [16, 28, 45, 48, 138, 533, 600, 699, 713], "enumer": 16, "requir": [16, 78, 84, 85, 94, 105, 106, 131, 133, 134, 136, 139, 143, 146, 147, 218, 278, 291, 292, 453, 544, 546, 571, 601, 607, 697, 717, 725, 756, 762, 796, 816, 840, 875, 877, 881], "suppress_sequ": [16, 66], "zero_index": [16, 66], "wrapper": [16, 66, 84, 85, 817], "otherwis": [16, 29, 45, 48, 57, 72, 73, 136, 138, 141, 144, 145, 190, 275, 341, 394, 451, 492, 495, 496, 498, 503, 508, 548, 549, 551, 556, 560, 572, 573, 575, 580, 585, 588, 604, 792, 877], "inform": [16, 47, 55, 59, 71, 86, 94, 132, 133, 134, 135, 136, 137, 138, 144, 145, 147, 193, 219, 221, 271, 280, 338, 343, 390, 396, 446, 455, 490, 493, 515, 521, 564, 569, 590, 596, 620, 664, 698, 710, 711, 720, 726, 727, 791, 812, 840, 877, 881], "NOT": [16, 88, 190], "meaning": [16, 45, 48, 54, 718, 877], "zhao": [16, 66], "mengyao": [16, 66], "wan": [16, 66], "ping": [16, 66], "lee": [16, 66, 69], "erik": [16, 66], "garrison": [16, 66], "gabor": [16, 66], "marth": [16, 66], "simd": [16, 66], "applic": [16, 47, 60, 66, 759, 881], "plo": [16, 66, 84, 85, 539, 545], "ONE": [16, 66], "2013": [16, 66, 76, 94, 543, 709], "web": [16, 60, 63, 66, 134, 147, 599, 600, 601, 602, 603], "juli": [16, 66], "2014": [16, 66, 132, 143, 533, 543], "http": [16, 47, 60, 61, 62, 63, 64, 65, 66, 69, 73, 83, 108, 131, 132, 133, 134, 135, 136, 137, 138, 141, 143, 144, 145, 146, 147, 281, 289, 290, 516, 539, 543, 545, 547, 565, 571, 583, 591, 599, 600, 601, 602, 603, 709, 813, 814, 839], "www": [16, 60, 63, 66, 83, 108, 131, 132, 133, 134, 135, 136, 137, 138, 143, 147, 281, 289, 290, 600], "ploson": [16, 66], "org": [16, 66, 108, 131, 136, 137, 138, 143, 145, 146, 516, 539, 543, 545, 547, 565, 571, 583, 591, 599, 600, 601, 602, 603, 709, 814], "articl": [16, 66, 134], "info": [16, 66, 203, 222, 293, 344, 397, 456, 608, 664], "doi": [16, 66, 135, 137, 539, 545, 814], "10": [16, 47, 66, 69, 84, 85, 133, 135, 136, 137, 138, 139, 141, 142, 143, 193, 203, 218, 222, 247, 293, 317, 344, 368, 397, 422, 456, 528, 533, 539, 545, 603, 698, 723, 726, 727, 814, 881], "1371": [16, 66, 539, 545], "journal": [16, 66, 69, 72, 79, 94, 95, 97, 99, 138, 539, 545, 599], "pone": [16, 66], "0082138": [16, 66], "alignmentstructur": 17, "positional_metadata": [28, 33, 46, 52, 53, 54, 136, 146, 222, 227, 239, 240, 243, 259, 265, 272, 273, 293, 298, 310, 313, 327, 332, 339, 344, 349, 361, 364, 378, 384, 391, 397, 402, 414, 415, 418, 434, 440, 447, 448, 456, 461, 473, 480, 485, 491, 877], "sourc": [28, 29, 30, 31, 32, 33, 35, 38, 40, 42, 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, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 135, 136, 138, 139, 149, 150, 160, 161, 162, 163, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 190, 191, 192, 193, 194, 200, 202, 203, 204, 205, 206, 212, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 229, 232, 234, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 300, 303, 305, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 351, 354, 356, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 404, 407, 409, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 463, 466, 468, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 498, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 523, 524, 526, 527, 528, 529, 530, 531, 532, 533, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 547, 548, 549, 551, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571, 572, 573, 575, 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591, 592, 593, 594, 595, 596, 597, 598, 599, 600, 601, 602, 603, 604, 605, 607, 609, 619, 620, 630, 631, 641, 642, 652, 653, 663, 664, 674, 675, 685, 686, 696, 697, 699, 708, 709, 710, 711, 712, 713, 714, 715, 716, 717, 718, 719, 720, 721, 722, 724, 725, 726, 727, 728, 729, 730, 731, 732, 733, 734, 735, 736, 739, 743, 745, 748, 749, 750, 751, 752, 753, 754, 755, 756, 757, 758, 759, 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, 775, 776, 777, 778, 779, 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791, 792, 793, 794, 795, 796, 797, 798, 799, 800, 801, 802, 803, 804, 805, 806, 807, 808, 809, 810, 811, 812, 813, 814, 815, 816, 817, 818, 819, 820, 824, 831, 837, 838, 839, 840, 841, 851, 852, 853, 863, 864, 874], "store": [28, 38, 43, 51, 52, 53, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 193, 203, 222, 257, 259, 293, 325, 327, 344, 376, 378, 397, 432, 434, 456, 479, 480, 516, 546, 547, 565, 571, 591, 604, 620, 653, 664, 699, 712, 713, 718, 720, 734, 876, 877], "tabular": [28, 132, 133, 145, 147], "iter": [28, 38, 43, 48, 53, 60, 61, 62, 63, 64, 65, 66, 67, 103, 107, 108, 111, 144, 193, 214, 215, 216, 218, 229, 232, 237, 240, 248, 262, 272, 275, 300, 303, 308, 310, 318, 329, 339, 341, 351, 354, 359, 361, 369, 381, 391, 394, 404, 407, 412, 415, 423, 437, 447, 451, 463, 466, 471, 473, 476, 482, 491, 492, 494, 505, 508, 510, 512, 520, 528, 558, 560, 561, 568, 582, 585, 586, 595, 600, 603, 604, 697, 709, 726, 727, 735, 736, 743, 760, 763, 764, 773, 781, 784, 787, 788, 789, 797, 798, 804, 807, 837, 839, 841, 863, 879, 881], "grammaredsequ": [28, 38, 43, 45, 48, 49, 60, 63, 134, 136, 143, 146, 222, 243, 246, 274, 344, 364, 367, 393, 397, 418, 421, 450], "exampl": [28, 29, 30, 31, 32, 33, 38, 40, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 56, 57, 58, 78, 105, 106, 107, 140, 145, 148, 160, 161, 162, 191, 193, 203, 215, 220, 222, 223, 224, 227, 229, 232, 234, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 272, 273, 275, 276, 277, 278, 279, 281, 282, 290, 291, 292, 293, 294, 295, 298, 300, 303, 305, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 339, 341, 342, 344, 345, 346, 349, 351, 354, 356, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 391, 392, 394, 395, 397, 398, 399, 402, 404, 407, 409, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 447, 448, 449, 451, 452, 453, 454, 456, 457, 458, 461, 463, 466, 468, 470, 471, 472, 473, 474, 475, 476, 477, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 491, 492, 494, 505, 506, 509, 512, 514, 517, 520, 523, 524, 526, 527, 528, 529, 530, 531, 532, 533, 534, 535, 536, 537, 539, 540, 541, 542, 543, 544, 545, 547, 558, 563, 566, 568, 582, 589, 592, 593, 595, 599, 600, 601, 602, 603, 604, 605, 606, 607, 697, 709, 718, 725, 726, 727, 728, 735, 736, 748, 749, 750, 751, 752, 754, 755, 756, 757, 758, 759, 760, 761, 763, 764, 765, 766, 767, 768, 769, 770, 772, 773, 774, 775, 778, 779, 780, 781, 782, 783, 784, 786, 787, 788, 789, 790, 792, 793, 794, 795, 796, 797, 798, 799, 800, 801, 803, 804, 805, 806, 807, 808, 809, 810, 811, 813, 814, 815, 816, 817, 819, 839, 874, 875], "arbitrari": [28, 46, 49, 140, 145, 146, 222, 344, 397, 456, 697, 840, 877], "shallow": [28, 31, 203, 204, 225, 296, 347, 400, 456, 459], "copi": [28, 31, 32, 136, 143, 146, 203, 204, 205, 225, 226, 272, 296, 297, 339, 347, 348, 391, 400, 401, 447, 456, 459, 460, 491, 516, 519, 547, 565, 567, 591, 594, 721, 728, 735, 736, 763, 795, 796, 802, 810, 811, 834, 835, 836], "made": [28, 90, 456, 528, 547, 571, 697, 750, 767, 768, 790, 816], "consum": [28, 48, 162, 222, 281, 344, 397, 456], "abl": [28, 48, 108, 222, 344, 397, 456, 528, 726, 764], "directli": [28, 45, 48, 145, 222, 281, 344, 397, 456, 522, 528, 607, 840, 881], "constructor": [28, 45, 48, 56, 134, 136, 137, 138, 143, 144, 146, 161, 174, 185, 222, 265, 281, 332, 344, 384, 397, 440, 456, 485, 494, 605], "label": [28, 30, 33, 35, 45, 48, 49, 54, 56, 57, 58, 134, 136, 138, 143, 145, 146, 514, 543, 546, 563, 589, 599, 600, 602, 603, 604, 699, 709, 754, 818], "content": [28, 46, 135, 136, 137, 138, 139, 141, 145, 148, 160, 161, 162, 222, 239, 240, 243, 246, 273, 277, 310, 313, 316, 361, 364, 367, 397, 414, 415, 418, 421, 448, 449, 473, 877], "hashabl": [28, 30, 697, 863], "rais": [28, 45, 47, 48, 50, 54, 56, 58, 69, 78, 79, 80, 94, 103, 105, 106, 107, 111, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 136, 137, 143, 148, 149, 160, 161, 162, 181, 182, 183, 184, 186, 187, 188, 217, 224, 240, 241, 245, 247, 249, 260, 261, 263, 264, 266, 267, 268, 269, 275, 291, 293, 295, 310, 311, 315, 317, 319, 328, 330, 331, 333, 334, 335, 336, 341, 346, 361, 362, 366, 368, 370, 380, 382, 383, 385, 386, 387, 388, 394, 399, 415, 416, 420, 422, 424, 435, 436, 438, 439, 441, 442, 443, 444, 451, 458, 473, 474, 475, 477, 481, 483, 484, 486, 487, 488, 489, 492, 498, 505, 506, 508, 509, 510, 513, 520, 523, 524, 530, 537, 538, 544, 551, 558, 560, 561, 562, 568, 575, 582, 585, 586, 587, 595, 599, 600, 601, 603, 604, 642, 686, 697, 709, 712, 713, 718, 726, 727, 728, 749, 756, 757, 759, 762, 764, 765, 767, 768, 770, 772, 774, 780, 782, 785, 795, 796, 797, 798, 803, 808, 817, 818, 819, 820], "valueerror": [28, 45, 47, 48, 50, 54, 56, 58, 69, 78, 80, 94, 103, 105, 106, 107, 111, 181, 186, 240, 241, 247, 249, 260, 263, 264, 266, 267, 268, 269, 275, 291, 293, 310, 311, 317, 319, 328, 330, 331, 333, 334, 335, 336, 341, 361, 362, 368, 370, 380, 382, 383, 385, 386, 387, 388, 394, 415, 416, 422, 424, 435, 438, 439, 441, 442, 443, 444, 451, 456, 473, 474, 477, 481, 483, 484, 486, 487, 488, 489, 492, 506, 509, 510, 523, 524, 530, 537, 538, 544, 561, 586, 600, 601, 603, 604, 642, 686, 697, 709, 712, 713, 726, 727, 728, 757, 759, 764, 772, 780, 782, 785, 797, 798, 803, 808, 819], "both": [28, 46, 54, 56, 67, 72, 73, 74, 78, 94, 131, 132, 133, 136, 137, 143, 145, 147, 181, 186, 218, 291, 510, 531, 532, 534, 535, 546, 561, 586, 588, 593, 600, 601, 602, 603, 718, 758, 759, 798, 807, 875, 877], "typeerror": [28, 45, 48, 54, 103, 181, 182, 186, 187, 224, 240, 241, 245, 249, 260, 261, 266, 267, 268, 269, 295, 310, 311, 315, 319, 328, 333, 334, 335, 336, 346, 361, 362, 366, 370, 380, 385, 386, 387, 388, 399, 415, 416, 420, 424, 435, 436, 441, 442, 443, 444, 458, 473, 474, 475, 477, 481, 486, 487, 488, 489, 523, 524, 600, 601, 603, 726, 727, 728, 756], "isn": [28, 45, 48, 54, 80, 145, 146, 160, 162, 191, 193, 534, 535, 728], "doe": [28, 45, 46, 48, 54, 57, 66, 78, 94, 132, 134, 136, 137, 139, 141, 143, 146, 190, 240, 281, 282, 288, 291, 310, 361, 415, 473, 506, 516, 523, 546, 565, 588, 591, 599, 601, 603, 642, 718, 726, 727, 750, 759, 770, 783, 796, 803, 806, 813, 817, 875], "exactli": [28, 45, 48, 53, 63, 64, 65, 136, 137, 143, 148, 227, 236, 282, 298, 307, 349, 358, 402, 411, 461, 470, 544, 709, 752], "reassign_index": [28, 45, 48, 57, 58, 143], "neither": [28, 56, 191, 798, 807], "nor": [28, 45, 48, 56, 140, 143, 547, 798], "rangeindex": [28, 45, 48, 56, 143], "stop": [28, 45, 48, 56, 69, 143, 241, 260, 278, 279, 281, 291, 292, 311, 328, 344, 362, 379, 380, 416, 435, 453, 454, 474, 481, 754, 841, 877], "four": [28, 137, 146, 222, 344, 397, 528, 709], "acgt": [28, 45, 48, 49, 51, 52, 58, 223, 227, 236, 240, 251, 252, 257, 259, 261, 265, 294, 298, 307, 310, 325, 327, 332, 345, 349, 358, 361, 376, 378, 384, 398, 402, 411, 415, 426, 427, 432, 434, 436, 440, 456, 457, 461, 470, 473, 479, 480, 485, 494, 512], "ag": [28, 45, 48, 50, 546, 725, 726], "wasn": [28, 137], "non": [28, 72, 80, 132, 134, 135, 139, 145, 193, 222, 258, 270, 274, 293, 326, 337, 340, 344, 377, 389, 393, 397, 433, 445, 450, 494, 525, 526, 527, 528, 530, 533, 537, 538, 540, 541, 542, 571, 599, 602, 603, 607, 712, 718, 723, 758, 759, 764], "seq3": [28, 48, 136, 143], "prob": [28, 33, 46, 53], "iloc": [28, 35], "slice": [28, 35, 229, 247, 248, 262, 272, 300, 317, 318, 329, 339, 351, 368, 369, 381, 391, 404, 422, 423, 437, 447, 463, 476, 482, 491, 498, 546, 551, 575, 739, 877], "axi": [28, 35, 50, 80, 96, 140, 222, 293, 344, 397, 456, 494, 642, 686, 699, 709, 717, 724, 727, 818], "along": [28, 140, 222, 293, 344, 397, 456, 709, 717, 718], "loc": [28, 35, 456, 528, 726], "shape": [28, 40, 49, 131, 142, 494, 496, 526, 527, 529, 530, 531, 532, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 545, 547, 549, 571, 573, 601, 714, 717, 728], "boolean": [29, 106, 136, 139, 144, 193, 222, 229, 242, 244, 247, 250, 262, 265, 267, 269, 270, 272, 300, 312, 314, 317, 320, 329, 332, 334, 336, 337, 339, 344, 351, 363, 365, 368, 371, 381, 384, 386, 388, 389, 391, 392, 397, 404, 417, 419, 422, 425, 437, 440, 442, 444, 445, 447, 456, 463, 482, 485, 487, 489, 491, 586], "OR": 29, "acg": [29, 30, 31, 32, 33, 38, 40, 43, 50, 53, 54, 56, 57, 144, 146, 260, 263, 328, 330, 380, 382, 435, 438, 481, 483], "ac": [29, 30, 31, 32, 33, 38, 40, 43, 46, 48, 50, 54, 56, 57, 60, 63, 135, 137, 138, 146, 193, 250, 320, 371, 425, 877], "No": [29, 73, 132, 133, 135, 144, 147, 203, 238, 309, 360, 413, 472, 601], "search": [30, 60, 132, 133, 136, 218, 247, 260, 317, 328, 368, 380, 422, 435, 481, 495, 548, 572, 713, 762, 767, 768, 769, 770, 837, 877], "l1": 30, "l2": 30, "l3": 30, "__deepcopy__": [31, 204], "msa_copi": [31, 32], "memo": [32, 205, 226, 297, 348, 401, 460], "deep": [32, 70, 205, 225, 226, 296, 297, 347, 348, 400, 401, 456, 459, 460, 507, 519, 559, 567, 584, 594], "__copy__": [32, 205], "deepcopi": [32, 735, 736, 760, 810, 811], "against": [33, 42, 60, 63, 137, 194, 200, 206, 212, 227, 236, 282, 288, 298, 307, 349, 358, 402, 411, 461, 470, 528, 607, 757], "pleas": [35, 55, 59, 136, 144, 219, 221, 271, 280, 338, 343, 390, 396, 446, 455, 490, 493, 515, 521, 564, 569, 590, 596, 710, 711, 791, 812], "restrict": [35, 78, 105, 106, 143, 877], "over": [38, 43, 53, 108, 136, 137, 144, 145, 146, 232, 237, 303, 308, 354, 359, 407, 412, 466, 471, 494, 533, 605, 619, 641, 652, 685, 696, 723, 724, 743, 781, 784, 787, 788, 789, 801, 804, 807, 879], "yield": [38, 43, 53, 136, 218, 232, 237, 246, 247, 248, 262, 263, 279, 292, 303, 308, 316, 317, 318, 329, 330, 354, 359, 367, 368, 369, 381, 382, 407, 412, 421, 422, 423, 437, 438, 454, 466, 471, 476, 482, 483, 603, 769, 781, 784, 787, 788, 789, 798, 804, 806, 807, 841, 875, 881], "size": [40, 76, 494, 533, 547, 571, 599, 600, 601, 603, 686, 697, 709, 717, 723, 725, 726, 727, 839], "1st": [40, 675, 819], "dimens": [40, 142, 143, 494, 504, 526, 530, 534, 535, 547, 557, 571, 581, 603, 699, 708, 709, 718, 719], "equival": [40, 76, 78, 94, 137, 145, 225, 226, 249, 251, 272, 273, 279, 292, 296, 297, 319, 339, 347, 348, 370, 391, 400, 401, 424, 426, 447, 448, 454, 459, 460, 477, 491, 505, 520, 523, 528, 558, 568, 582, 595, 601, 877], "inequ": [42, 200, 212, 236, 288, 307, 358, 411, 470, 571, 718], "__eq__": [42, 212, 503, 556, 580], "revers": [43, 53, 57, 148, 237, 239, 261, 273, 279, 291, 292, 308, 359, 412, 414, 436, 448, 449, 454, 471, 599, 603, 798, 877, 881], "summari": [44, 504, 528, 557, 581], "reset_index": [45, 48], "without": [45, 48, 54, 56, 90, 106, 133, 141, 143, 145, 146, 456, 525, 697, 709, 727, 728, 765, 774, 806, 839, 840, 875], "recomput": [45, 48, 54], "treat": [45, 46, 47, 48, 136, 140, 145, 222, 265, 274, 332, 340, 344, 384, 393, 397, 440, 450, 456, 485, 523, 726], "reset": [45, 48, 56], "choic": [45, 48, 140, 718], "necessarili": [45, 48, 54, 142, 249, 319, 370, 424, 456, 477, 728], "own": [45, 48, 54, 131, 136, 142, 146, 148, 723], "via": [45, 48, 56, 69, 84, 85, 136, 143, 245, 281, 282, 288, 315, 366, 420, 475, 599, 601, 602], "acga": [45, 48, 227, 236, 298, 307, 349, 358, 402, 411, 461, 470], "major": [46, 525, 593, 813], "most": [46, 70, 79, 94, 131, 134, 136, 137, 140, 141, 143, 145, 147, 291, 456, 601, 697, 720, 723, 774, 776, 813, 879], "common": [46, 51, 52, 63, 78, 94, 132, 136, 137, 138, 145, 146, 147, 257, 259, 325, 327, 376, 378, 432, 434, 479, 480, 526, 547, 642, 734, 759, 767, 780, 782, 805, 806, 814, 877, 879, 880], "ti": [46, 70, 813], "broken": [46, 813], "manner": [46, 136, 143, 229, 243, 300, 313, 351, 364, 404, 418, 463, 601, 718], "present": [46, 47, 78, 105, 106, 132, 136, 142, 145, 146, 204, 205, 222, 239, 242, 243, 244, 249, 250, 260, 270, 273, 291, 312, 313, 314, 319, 320, 328, 337, 344, 363, 364, 365, 370, 371, 380, 389, 392, 397, 414, 417, 418, 419, 424, 425, 435, 445, 448, 477, 481, 508, 528, 560, 585, 599, 600, 602, 603, 642, 708, 718, 727, 728, 758, 813, 814, 816, 879], "default_gap_char": [46, 47, 54, 222, 293, 344, 397], "distinct": [46, 91, 92, 101, 523, 546], "contribut": [46, 94, 607, 712, 717], "AT": [46, 136, 137, 143], "tt": [46, 262, 329, 381, 437, 482], "cg": [46, 272, 339, 391, 447, 456, 491], "degener": [46, 47, 135, 136, 137, 138, 139, 222, 239, 240, 242, 243, 246, 251, 252, 253, 254, 258, 270, 273, 274, 276, 277, 278, 279, 281, 291, 292, 293, 310, 312, 313, 316, 321, 322, 326, 337, 340, 342, 344, 361, 363, 364, 367, 372, 373, 377, 389, 393, 395, 397, 414, 415, 417, 418, 421, 426, 427, 428, 429, 433, 445, 448, 449, 450, 452, 453, 454, 473, 506, 877], "gc": [46, 135, 136, 137, 138, 139, 147, 222, 239, 240, 243, 246, 252, 273, 277, 282, 292, 310, 313, 316, 361, 364, 367, 397, 414, 415, 418, 421, 427, 448, 449, 473, 877], "33": [46, 78, 105, 106, 137, 246, 316, 367, 421, 533, 600, 603, 723, 726, 877], "last": [46, 135, 143, 262, 291, 329, 381, 437, 456, 482, 601, 698, 881], "metric": [47, 69, 74, 78, 79, 94, 103, 104, 105, 106, 107, 108, 109, 110, 111, 137, 245, 315, 366, 420, 475, 510, 524, 561, 571, 586, 734, 874, 877], "inverse_shannon_uncertainti": 47, "degenerate_mod": 47, "gap_mod": 47, "nan": [47, 50, 54, 85, 132, 145, 240, 249, 310, 319, 361, 370, 415, 424, 473, 477, 523, 524, 599, 600, 601, 602, 603, 604, 607, 709, 725, 726, 805, 817], "larger": [47, 726], "mode": [47, 148, 190, 291, 727, 840], "handl": [47, 54, 136, 137, 144, 146, 147, 148, 150, 160, 162, 190, 291, 292, 528, 601, 603, 604, 723, 807, 814, 839, 881], "assign": [47, 56, 67, 103, 107, 143, 145, 194, 272, 339, 391, 447, 456, 491, 512, 528, 533, 599, 602, 603, 697, 727, 753, 754, 755], "np": [47, 50, 78, 85, 94, 105, 106, 132, 222, 224, 241, 242, 244, 245, 249, 250, 260, 261, 266, 267, 268, 269, 270, 275, 295, 311, 312, 314, 315, 319, 320, 328, 333, 334, 335, 336, 337, 341, 344, 346, 362, 363, 365, 366, 370, 371, 380, 385, 386, 387, 388, 389, 392, 394, 397, 399, 416, 417, 419, 420, 424, 425, 435, 436, 441, 442, 443, 444, 445, 451, 456, 458, 474, 475, 477, 481, 486, 487, 488, 489, 492, 494, 523, 524, 526, 527, 529, 530, 531, 532, 533, 534, 535, 536, 537, 539, 540, 541, 542, 543, 545, 546, 599, 601, 602, 603, 604, 607, 608, 697, 698, 709, 722, 723, 725, 726, 727, 728, 776, 798, 813, 817], "remov": [47, 66, 78, 94, 105, 106, 136, 140, 143, 216, 243, 274, 313, 340, 364, 393, 418, 450, 751, 766, 786, 790, 793, 797, 808, 877], "up": [47, 67, 134, 143, 145, 146, 190, 203, 215, 453, 454, 498, 530, 537, 538, 540, 541, 542, 551, 575, 601, 697, 727, 751, 756, 759, 790, 796, 863, 879], "float": [47, 50, 60, 61, 62, 63, 64, 65, 66, 67, 78, 83, 84, 94, 103, 105, 106, 107, 108, 111, 131, 132, 138, 140, 141, 145, 245, 251, 252, 266, 268, 315, 333, 335, 366, 385, 387, 420, 426, 427, 441, 443, 475, 486, 488, 510, 512, 523, 524, 528, 533, 537, 538, 542, 545, 546, 547, 561, 586, 601, 603, 605, 607, 620, 664, 709, 724, 726, 727, 734, 749, 757, 758, 759, 764, 765, 774, 805, 813, 817], "unknown": [47, 84, 85, 130, 138, 193, 247, 317, 368, 422, 697], "mislead": [47, 111], "point": [47, 80, 83, 85, 131, 134, 145, 148, 161, 193, 265, 272, 275, 332, 339, 341, 384, 391, 394, 440, 447, 451, 485, 491, 492, 506, 603, 609, 631, 686, 709, 726, 727, 796, 817, 838], "out": [47, 144, 145, 148, 709, 758, 759, 881], "compos": [47, 137, 144], "90": [47, 139, 533, 881], "tryptophan": [47, 344], "would": [47, 78, 80, 83, 105, 106, 134, 136, 139, 141, 143, 145, 146, 148, 240, 262, 310, 329, 361, 381, 415, 437, 473, 482, 505, 540, 543, 558, 582, 607, 725, 726, 756, 806, 807, 813, 875], "highli": 47, "alanin": [47, 344], "glycin": [47, 344], "recod": 47, "awar": [47, 94, 145, 456], "consid": [47, 69, 78, 83, 94, 105, 106, 136, 141, 227, 262, 298, 329, 349, 381, 402, 437, 461, 482, 523, 525, 540, 603, 604, 697, 725, 726, 727, 817, 840], "simpli": [47, 54, 101, 148, 281, 516, 565, 591, 718, 723, 767, 881], "minu": [47, 138, 146, 675], "shannon": [47, 82, 95], "uncertainti": [47, 533, 607], "invers": [47, 527, 532, 535, 541], "impli": [47, 190, 607], "higher": [47, 494, 528, 533, 852], "entropi": [47, 82, 97], "make": [47, 54, 136, 141, 145, 148, 282, 498, 523, 551, 575, 599, 603, 727, 802, 805, 806, 814, 820, 840, 881], "symbol": [47, 136], "done": [47, 528, 603, 630, 663, 674], "prefer": [47, 103, 107, 137, 712, 713], "valdar": 47, "residu": [47, 720], "2002": [47, 78, 94, 102, 133, 136], "schneider": 47, "pitfal": 47, "theori": [47, 71, 86, 97, 539, 545], "websit": 47, "ca": [47, 142, 699, 713, 720], "2015": [47, 525, 528, 539, 545], "ncifcrf": 47, "gov": [47, 61, 62, 64, 65, 132, 133, 136, 138, 144, 147, 281, 289, 290], "glossari": 47, "html": [47, 83, 132, 134, 136, 138, 141, 143, 146, 193, 516, 547, 565, 571, 583, 591, 599, 600, 601, 602, 603, 709, 813], "shannon_entropi": 47, "classmethod": [49, 55, 215, 219, 240, 271, 290, 310, 338, 361, 390, 415, 446, 473, 490, 506, 509, 510, 511, 512, 515, 561, 564, 586, 590, 710, 771, 772, 773, 791], "dictionari": [49, 51, 56, 58, 67, 146, 147, 150, 193, 204, 205, 214, 218, 257, 325, 376, 432, 456, 479, 509, 518, 601, 772], "construct": [49, 58, 138, 147, 193, 194, 222, 293, 344, 397, 494, 509, 512, 518, 539, 546, 698, 762, 772, 773, 814, 874, 875, 879], "to_dict": 49, "sort": [49, 54, 109, 110, 194, 203, 206, 246, 249, 275, 316, 319, 341, 367, 370, 394, 421, 424, 451, 477, 492, 642, 675, 697, 800, 805, 806, 813, 877, 881], "rel": [50, 94, 135, 138, 249, 251, 252, 264, 266, 268, 319, 331, 333, 335, 370, 383, 385, 387, 424, 426, 427, 439, 441, 443, 477, 484, 486, 488, 539, 545, 583, 799, 817, 852, 877], "across": [50, 94, 136, 137, 143, 203, 528, 533, 601, 726, 813], "1d": [50, 103, 222, 224, 229, 241, 242, 244, 245, 247, 248, 250, 260, 261, 262, 266, 267, 268, 269, 270, 272, 275, 295, 300, 311, 312, 314, 315, 317, 318, 320, 328, 329, 333, 334, 335, 336, 337, 339, 341, 344, 346, 351, 362, 363, 365, 366, 368, 369, 371, 380, 381, 385, 386, 387, 388, 389, 391, 392, 394, 397, 399, 404, 416, 417, 419, 420, 422, 423, 425, 435, 436, 437, 441, 442, 443, 444, 445, 447, 451, 456, 458, 463, 474, 475, 476, 481, 482, 486, 487, 488, 489, 491, 492], "ndarrai": [50, 107, 222, 224, 241, 242, 244, 245, 250, 260, 261, 266, 267, 268, 269, 270, 275, 295, 311, 312, 314, 315, 320, 328, 333, 334, 335, 336, 337, 341, 344, 346, 362, 363, 365, 366, 371, 380, 385, 386, 387, 388, 389, 392, 394, 397, 399, 416, 417, 419, 420, 425, 435, 436, 441, 442, 443, 444, 445, 451, 456, 458, 474, 475, 481, 486, 487, 488, 489, 492, 498, 516, 526, 527, 529, 530, 531, 532, 534, 535, 536, 537, 538, 540, 541, 542, 543, 547, 551, 565, 575, 583, 588, 591, 605, 607, 721, 728, 771], "vector": [50, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 105, 106, 140, 242, 244, 247, 250, 262, 265, 267, 269, 270, 272, 275, 281, 312, 314, 317, 320, 329, 332, 334, 336, 337, 339, 341, 363, 365, 368, 371, 381, 384, 386, 388, 389, 391, 392, 394, 417, 419, 422, 425, 437, 440, 442, 444, 445, 447, 451, 482, 485, 487, 489, 491, 492, 498, 526, 527, 528, 533, 534, 535, 540, 541, 542, 545, 546, 547, 551, 571, 575, 599, 602, 603, 653, 713, 727, 728, 805, 874], "specifi": [50, 54, 94, 111, 132, 134, 136, 137, 138, 139, 140, 143, 146, 147, 148, 180, 190, 193, 203, 216, 218, 222, 229, 247, 249, 265, 278, 290, 291, 293, 300, 317, 319, 332, 344, 351, 368, 370, 384, 397, 404, 422, 424, 440, 453, 456, 463, 477, 485, 495, 498, 505, 508, 513, 514, 520, 526, 527, 528, 533, 534, 535, 537, 538, 544, 548, 551, 558, 560, 562, 563, 568, 572, 575, 582, 585, 587, 589, 595, 599, 600, 601, 602, 603, 607, 686, 709, 717, 718, 724, 756, 764, 795, 798, 800, 803, 806, 813, 840, 852, 853, 863, 874, 881], "Will": [50, 180, 183, 188, 190, 507, 519, 559, 567, 584, 594, 699, 728], "least": [51, 52, 90, 141, 145, 247, 256, 257, 259, 317, 324, 325, 327, 368, 375, 376, 378, 422, 431, 432, 434, 478, 479, 480, 528, 601, 709, 726, 727, 816, 881], "demonstr": [51, 52, 148, 257, 259, 325, 327, 376, 378, 432, 434, 479, 480], "behavior": [51, 52, 54, 60, 61, 62, 136, 137, 138, 145, 190, 257, 259, 275, 291, 325, 327, 341, 376, 378, 394, 432, 434, 451, 456, 479, 480, 492, 599, 601, 603, 758, 881], "rang": [52, 74, 83, 95, 106, 137, 138, 145, 239, 243, 249, 259, 262, 273, 313, 319, 327, 329, 364, 370, 378, 381, 414, 418, 424, 434, 437, 448, 477, 480, 482, 599, 600, 709, 727, 776, 881], "qualiti": [52, 136, 144, 222, 227, 239, 243, 259, 273, 298, 313, 327, 344, 349, 364, 378, 397, 402, 414, 418, 434, 448, 456, 461, 480, 709, 877], "ignore_metadata": 53, "improv": [53, 141, 143, 222, 344, 397, 586], "__iter__": 53, "__reversed__": 53, "concat": [53, 54], "artifact": [53, 60, 61, 62], "real": [53, 136, 137, 144, 525, 526, 527, 531, 532, 534, 535, 540, 541, 542], "concaten": [53, 146, 215, 240, 310, 361, 415, 473], "outer": [53, 54, 240, 310, 361, 415, 473, 509], "join": [53, 132, 133, 137, 144, 146, 147, 240, 310, 361, 415, 473, 806, 813, 814], "aa": [53, 136, 138, 143, 281], "gt": 53, "strict": [54, 143, 240, 310, 361, 415, 473, 508, 560, 585, 601, 604, 607], "horizont": 54, "control": [54, 136, 599, 601, 602, 608, 720, 723, 725, 726, 727], "dure": [54, 136, 194, 240, 310, 361, 415, 473, 603, 838], "section": [54, 136, 137, 142, 145, 146, 281, 456, 600, 601, 712, 713], "inner": [54, 141, 240, 310, 361, 415, 473, 509], "left": [54, 69, 97, 141, 526, 527, 531, 536, 540, 541, 542, 543, 754, 776, 817, 818, 879], "right": [54, 69, 97, 141, 525, 526, 527, 531, 536, 540, 541, 542, 543, 776, 817, 818, 881], "unshar": 54, "pad": [54, 143, 240, 310, 361, 415, 473], "guarante": [54, 85, 145, 222, 246, 316, 344, 367, 397, 421, 547, 605, 764], "duplic": [54, 111, 137, 145, 146, 217, 275, 341, 394, 451, 492, 508, 560, 585, 729, 837], "doesn": [54, 136, 145, 184, 291, 540, 544, 598, 712, 718, 722, 796, 815, 880], "subclass": 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115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 137, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 161, 174, 181, 182, 183, 185, 186, 187, 188, 189, 190, 191, 192, 219, 221, 271, 280, 338, 343, 390, 396, 446, 455, 490, 493, 514, 515, 521, 528, 546, 563, 564, 569, 589, 590, 596, 630, 663, 674, 709, 710, 711, 725, 754, 791, 812, 838, 839, 874, 879], "kwarg": [55, 59, 66, 103, 107, 108, 111, 112, 160, 162, 174, 181, 182, 183, 185, 186, 187, 188, 191, 192, 219, 221, 271, 278, 279, 280, 338, 343, 390, 396, 446, 453, 454, 455, 490, 493, 494, 515, 521, 564, 569, 590, 596, 686, 710, 711, 791, 812, 840, 875], "instanc": [55, 59, 148, 162, 175, 177, 178, 179, 181, 186, 203, 218, 219, 221, 240, 271, 280, 310, 338, 343, 361, 390, 396, 415, 446, 455, 473, 490, 493, 496, 506, 515, 521, 523, 524, 533, 547, 549, 564, 569, 571, 573, 588, 590, 596, 601, 603, 604, 605, 619, 641, 652, 685, 696, 709, 710, 711, 727, 734, 750, 791, 812, 813, 820, 821, 824, 831, 879, 881], "registri": [55, 59, 136, 137, 144, 219, 221, 271, 280, 338, 343, 390, 396, 446, 455, 490, 493, 515, 521, 564, 569, 590, 596, 710, 711, 791, 812, 875], "system": [55, 59, 86, 97, 145, 147, 148, 203, 219, 221, 271, 280, 338, 343, 390, 396, 446, 455, 490, 493, 515, 521, 564, 569, 590, 596, 710, 711, 726, 791, 812], "clustal": [55, 59, 114, 875], "fasta": [55, 59, 116, 137, 139, 144, 271, 280, 338, 343, 390, 396, 446, 455, 490, 493, 875], "fastq": [55, 59, 117, 144, 271, 280, 338, 343, 390, 396, 446, 455, 490, 493, 875], "phylip": [55, 59, 126, 136, 141, 813, 875, 879], "stockholm": [55, 59, 129], "filepath": [55, 59, 181, 182, 183, 186, 187, 188, 190, 219, 221, 271, 280, 338, 343, 390, 396, 446, 455, 490, 493, 515, 521, 564, 569, 590, 596, 604, 710, 711, 791, 812], "url": [55, 59, 181, 182, 183, 186, 187, 188, 190, 219, 221, 271, 280, 338, 343, 390, 396, 446, 455, 490, 493, 515, 521, 564, 569, 590, 596, 710, 711, 791, 812], "filehandl": [55, 59, 148, 160, 161, 162, 181, 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\ No newline at end of file
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"generated/skbio.workflow.Workflow.__lt__.rst", "generated/skbio.workflow.Workflow.__ne__.rst", "generated/skbio.workflow.Workflow.__str__.rst", "generated/skbio.workflow.Workflow.initialize_state.rst", "generated/skbio.workflow.method.rst", "generated/skbio.workflow.method.__call__.rst", "generated/skbio.workflow.method.__eq__.rst", "generated/skbio.workflow.method.__ge__.rst", "generated/skbio.workflow.method.__getstate__.rst", "generated/skbio.workflow.method.__gt__.rst", "generated/skbio.workflow.method.__hash__.rst", "generated/skbio.workflow.method.__le__.rst", "generated/skbio.workflow.method.__lt__.rst", "generated/skbio.workflow.method.__ne__.rst", "generated/skbio.workflow.method.__str__.rst", "generated/skbio.workflow.requires.rst", "generated/skbio.workflow.requires.__call__.rst", "generated/skbio.workflow.requires.__eq__.rst", "generated/skbio.workflow.requires.__ge__.rst", "generated/skbio.workflow.requires.__getstate__.rst", "generated/skbio.workflow.requires.__gt__.rst", "generated/skbio.workflow.requires.__hash__.rst", "generated/skbio.workflow.requires.__le__.rst", "generated/skbio.workflow.requires.__lt__.rst", "generated/skbio.workflow.requires.__ne__.rst", "generated/skbio.workflow.requires.__str__.rst", "index.rst", "io.rst", "metadata.rst", "sequence.rst", "stats.rst", "tree.rst", "util.rst", "workflow.rst"], "titles": ["Alignments (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.alignment</span></code>)", "Diversity calculations (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.diversity</span></code>)", "skbio.alignment.AlignmentStructure", "skbio.alignment.AlignmentStructure.__eq__", "skbio.alignment.AlignmentStructure.__ge__", "skbio.alignment.AlignmentStructure.__getitem__", "skbio.alignment.AlignmentStructure.__getstate__", "skbio.alignment.AlignmentStructure.__gt__", "skbio.alignment.AlignmentStructure.__hash__", "skbio.alignment.AlignmentStructure.__le__", "skbio.alignment.AlignmentStructure.__lt__", "skbio.alignment.AlignmentStructure.__ne__", "skbio.alignment.AlignmentStructure.__setstate__", "skbio.alignment.AlignmentStructure.__str__", "skbio.alignment.AlignmentStructure.is_zero_based", "skbio.alignment.AlignmentStructure.set_zero_based", "skbio.alignment.StripedSmithWaterman", "skbio.alignment.StripedSmithWaterman.__call__", "skbio.alignment.StripedSmithWaterman.__eq__", "skbio.alignment.StripedSmithWaterman.__ge__", "skbio.alignment.StripedSmithWaterman.__getstate__", "skbio.alignment.StripedSmithWaterman.__gt__", "skbio.alignment.StripedSmithWaterman.__hash__", "skbio.alignment.StripedSmithWaterman.__le__", "skbio.alignment.StripedSmithWaterman.__lt__", "skbio.alignment.StripedSmithWaterman.__ne__", "skbio.alignment.StripedSmithWaterman.__setstate__", "skbio.alignment.StripedSmithWaterman.__str__", "skbio.alignment.TabularMSA", "skbio.alignment.TabularMSA.__bool__", "skbio.alignment.TabularMSA.__contains__", "skbio.alignment.TabularMSA.__copy__", "skbio.alignment.TabularMSA.__deepcopy__", "skbio.alignment.TabularMSA.__eq__", "skbio.alignment.TabularMSA.__ge__", "skbio.alignment.TabularMSA.__getitem__", "skbio.alignment.TabularMSA.__getstate__", "skbio.alignment.TabularMSA.__gt__", "skbio.alignment.TabularMSA.__iter__", "skbio.alignment.TabularMSA.__le__", "skbio.alignment.TabularMSA.__len__", "skbio.alignment.TabularMSA.__lt__", "skbio.alignment.TabularMSA.__ne__", "skbio.alignment.TabularMSA.__reversed__", "skbio.alignment.TabularMSA.__str__", "skbio.alignment.TabularMSA.append", "skbio.alignment.TabularMSA.consensus", "skbio.alignment.TabularMSA.conservation", "skbio.alignment.TabularMSA.extend", "skbio.alignment.TabularMSA.from_dict", "skbio.alignment.TabularMSA.gap_frequencies", "skbio.alignment.TabularMSA.has_metadata", "skbio.alignment.TabularMSA.has_positional_metadata", "skbio.alignment.TabularMSA.iter_positions", "skbio.alignment.TabularMSA.join", "skbio.alignment.TabularMSA.read", "skbio.alignment.TabularMSA.reassign_index", "skbio.alignment.TabularMSA.sort", "skbio.alignment.TabularMSA.to_dict", "skbio.alignment.TabularMSA.write", "skbio.alignment.global_pairwise_align", "skbio.alignment.global_pairwise_align_nucleotide", "skbio.alignment.global_pairwise_align_protein", "skbio.alignment.local_pairwise_align", "skbio.alignment.local_pairwise_align_nucleotide", "skbio.alignment.local_pairwise_align_protein", "skbio.alignment.local_pairwise_align_ssw", "skbio.alignment.make_identity_substitution_matrix", "Alpha diversity measures (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.diversity.alpha</span></code>)", "skbio.diversity.alpha.ace", "skbio.diversity.alpha.berger_parker_d", "skbio.diversity.alpha.brillouin_d", "skbio.diversity.alpha.chao1", "skbio.diversity.alpha.chao1_ci", "skbio.diversity.alpha.dominance", "skbio.diversity.alpha.doubles", "skbio.diversity.alpha.enspie", "skbio.diversity.alpha.esty_ci", "skbio.diversity.alpha.faith_pd", "skbio.diversity.alpha.fisher_alpha", "skbio.diversity.alpha.gini_index", "skbio.diversity.alpha.goods_coverage", "skbio.diversity.alpha.heip_e", "skbio.diversity.alpha.kempton_taylor_q", "skbio.diversity.alpha.lladser_ci", "skbio.diversity.alpha.lladser_pe", "skbio.diversity.alpha.margalef", "skbio.diversity.alpha.mcintosh_d", "skbio.diversity.alpha.mcintosh_e", "skbio.diversity.alpha.menhinick", "skbio.diversity.alpha.michaelis_menten_fit", "skbio.diversity.alpha.observed_features", "skbio.diversity.alpha.observed_otus", "skbio.diversity.alpha.osd", "skbio.diversity.alpha.phydiv", "skbio.diversity.alpha.pielou_e", "skbio.diversity.alpha.robbins", "skbio.diversity.alpha.shannon", "skbio.diversity.alpha.simpson", "skbio.diversity.alpha.simpson_e", "skbio.diversity.alpha.singles", "skbio.diversity.alpha.sobs", "skbio.diversity.alpha.strong", "skbio.diversity.alpha_diversity", "Beta diversity measures (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.diversity.beta</span></code>)", "skbio.diversity.beta.unweighted_unifrac", "skbio.diversity.beta.weighted_unifrac", "skbio.diversity.beta_diversity", "skbio.diversity.block_beta_diversity", "skbio.diversity.get_alpha_diversity_metrics", "skbio.diversity.get_beta_diversity_metrics", "skbio.diversity.partial_beta_diversity", "skbio.io.ArgumentOverrideWarning", "skbio.io.BLAST7FormatError", "skbio.io.ClustalFormatError", "skbio.io.EMBLFormatError", "skbio.io.FASTAFormatError", "skbio.io.FASTQFormatError", "skbio.io.FileFormatError", "skbio.io.FormatIdentificationWarning", "skbio.io.GFF3FormatError", "skbio.io.GenBankFormatError", "skbio.io.IOSourceError", "skbio.io.LSMatFormatError", "skbio.io.NewickFormatError", "skbio.io.OrdinationFormatError", "skbio.io.PhylipFormatError", "skbio.io.QSeqFormatError", "skbio.io.QUALFormatError", "skbio.io.StockholmFormatError", "skbio.io.UnrecognizedFormatError", "Simple binary dissimilarity matrix format (<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">skbio.io.format.binary_dm</span></code>)", "BIOM-Format (<code class=\"xref py py-mod docutils literal 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>)", "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.DuplicateRegistrationError", "skbio.io.registry.Format", "skbio.io.registry.Format.__eq__", "skbio.io.registry.Format.__ge__", "skbio.io.registry.Format.__getstate__", "skbio.io.registry.Format.__gt__", "skbio.io.registry.Format.__hash__", "skbio.io.registry.Format.__le__", "skbio.io.registry.Format.__lt__", "skbio.io.registry.Format.__ne__", "skbio.io.registry.Format.__str__", "skbio.io.registry.Format.reader", "skbio.io.registry.Format.sniffer", "skbio.io.registry.Format.writer", "skbio.io.registry.IORegistry", "skbio.io.registry.IORegistry.__eq__", "skbio.io.registry.IORegistry.__ge__", "skbio.io.registry.IORegistry.__getstate__", "skbio.io.registry.IORegistry.__gt__", "skbio.io.registry.IORegistry.__hash__", "skbio.io.registry.IORegistry.__le__", "skbio.io.registry.IORegistry.__lt__", "skbio.io.registry.IORegistry.__ne__", "skbio.io.registry.IORegistry.__str__", "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.InvalidRegistrationError", "skbio.io.registry.create_format", "skbio.io.registry.read", "skbio.io.registry.sniff", "skbio.io.registry.write", "I/O utils (<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.Interval", "skbio.metadata.Interval.__eq__", "skbio.metadata.Interval.__ge__", "skbio.metadata.Interval.__getstate__", "skbio.metadata.Interval.__gt__", "skbio.metadata.Interval.__le__", "skbio.metadata.Interval.__lt__", "skbio.metadata.Interval.__ne__", "skbio.metadata.Interval.__str__", "skbio.metadata.Interval.drop", "skbio.metadata.IntervalMetadata", "skbio.metadata.IntervalMetadata.__copy__", "skbio.metadata.IntervalMetadata.__deepcopy__", "skbio.metadata.IntervalMetadata.__eq__", "skbio.metadata.IntervalMetadata.__ge__", "skbio.metadata.IntervalMetadata.__getstate__", "skbio.metadata.IntervalMetadata.__gt__", "skbio.metadata.IntervalMetadata.__le__", "skbio.metadata.IntervalMetadata.__lt__", "skbio.metadata.IntervalMetadata.__ne__", "skbio.metadata.IntervalMetadata.__str__", "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.sequence.DNA", "skbio.sequence.DNA.__bool__", "skbio.sequence.DNA.__contains__", "skbio.sequence.DNA.__copy__", "skbio.sequence.DNA.__deepcopy__", "skbio.sequence.DNA.__eq__", "skbio.sequence.DNA.__ge__", "skbio.sequence.DNA.__getitem__", "skbio.sequence.DNA.__getstate__", "skbio.sequence.DNA.__gt__", "skbio.sequence.DNA.__iter__", "skbio.sequence.DNA.__le__", "skbio.sequence.DNA.__len__", "skbio.sequence.DNA.__lt__", "skbio.sequence.DNA.__ne__", "skbio.sequence.DNA.__reversed__", "skbio.sequence.DNA.__str__", "skbio.sequence.DNA.complement", "skbio.sequence.DNA.concat", "skbio.sequence.DNA.count", "skbio.sequence.DNA.definites", "skbio.sequence.DNA.degap", "skbio.sequence.DNA.degenerates", "skbio.sequence.DNA.distance", "skbio.sequence.DNA.expand_degenerates", "skbio.sequence.DNA.find_motifs", "skbio.sequence.DNA.find_with_regex", "skbio.sequence.DNA.frequencies", "skbio.sequence.DNA.gaps", "skbio.sequence.DNA.gc_content", "skbio.sequence.DNA.gc_frequency", "skbio.sequence.DNA.has_definites", "skbio.sequence.DNA.has_degenerates", "skbio.sequence.DNA.has_gaps", "skbio.sequence.DNA.has_interval_metadata", "skbio.sequence.DNA.has_metadata", "skbio.sequence.DNA.has_nondegenerates", "skbio.sequence.DNA.has_positional_metadata", "skbio.sequence.DNA.index", "skbio.sequence.DNA.is_reverse_complement", "skbio.sequence.DNA.iter_contiguous", "skbio.sequence.DNA.iter_kmers", "skbio.sequence.DNA.kmer_frequencies", "skbio.sequence.DNA.lowercase", "skbio.sequence.DNA.match_frequency", "skbio.sequence.DNA.matches", "skbio.sequence.DNA.mismatch_frequency", "skbio.sequence.DNA.mismatches", "skbio.sequence.DNA.nondegenerates", "skbio.sequence.DNA.read", "skbio.sequence.DNA.replace", "skbio.sequence.DNA.reverse_complement", "skbio.sequence.DNA.to_definites", "skbio.sequence.DNA.to_indices", "skbio.sequence.DNA.to_regex", "skbio.sequence.DNA.transcribe", "skbio.sequence.DNA.translate", "skbio.sequence.DNA.translate_six_frames", "skbio.sequence.DNA.write", "skbio.sequence.GeneticCode", "skbio.sequence.GeneticCode.__eq__", "skbio.sequence.GeneticCode.__ge__", "skbio.sequence.GeneticCode.__getstate__", "skbio.sequence.GeneticCode.__gt__", "skbio.sequence.GeneticCode.__le__", "skbio.sequence.GeneticCode.__lt__", "skbio.sequence.GeneticCode.__ne__", "skbio.sequence.GeneticCode.__str__", "skbio.sequence.GeneticCode.from_ncbi", "skbio.sequence.GeneticCode.translate", "skbio.sequence.GeneticCode.translate_six_frames", "skbio.sequence.GrammaredSequence", "skbio.sequence.GrammaredSequence.__bool__", "skbio.sequence.GrammaredSequence.__contains__", "skbio.sequence.GrammaredSequence.__copy__", "skbio.sequence.GrammaredSequence.__deepcopy__", "skbio.sequence.GrammaredSequence.__eq__", "skbio.sequence.GrammaredSequence.__ge__", "skbio.sequence.GrammaredSequence.__getitem__", "skbio.sequence.GrammaredSequence.__getstate__", "skbio.sequence.GrammaredSequence.__gt__", "skbio.sequence.GrammaredSequence.__iter__", "skbio.sequence.GrammaredSequence.__le__", "skbio.sequence.GrammaredSequence.__len__", "skbio.sequence.GrammaredSequence.__lt__", "skbio.sequence.GrammaredSequence.__ne__", "skbio.sequence.GrammaredSequence.__reversed__", "skbio.sequence.GrammaredSequence.__str__", "skbio.sequence.GrammaredSequence.concat", "skbio.sequence.GrammaredSequence.count", "skbio.sequence.GrammaredSequence.definites", "skbio.sequence.GrammaredSequence.degap", "skbio.sequence.GrammaredSequence.degenerates", "skbio.sequence.GrammaredSequence.distance", "skbio.sequence.GrammaredSequence.expand_degenerates", "skbio.sequence.GrammaredSequence.find_motifs", "skbio.sequence.GrammaredSequence.find_with_regex", "skbio.sequence.GrammaredSequence.frequencies", "skbio.sequence.GrammaredSequence.gaps", "skbio.sequence.GrammaredSequence.has_definites", "skbio.sequence.GrammaredSequence.has_degenerates", "skbio.sequence.GrammaredSequence.has_gaps", "skbio.sequence.GrammaredSequence.has_interval_metadata", "skbio.sequence.GrammaredSequence.has_metadata", "skbio.sequence.GrammaredSequence.has_nondegenerates", "skbio.sequence.GrammaredSequence.has_positional_metadata", "skbio.sequence.GrammaredSequence.index", "skbio.sequence.GrammaredSequence.iter_contiguous", "skbio.sequence.GrammaredSequence.iter_kmers", "skbio.sequence.GrammaredSequence.kmer_frequencies", "skbio.sequence.GrammaredSequence.lowercase", "skbio.sequence.GrammaredSequence.match_frequency", "skbio.sequence.GrammaredSequence.matches", "skbio.sequence.GrammaredSequence.mismatch_frequency", "skbio.sequence.GrammaredSequence.mismatches", "skbio.sequence.GrammaredSequence.nondegenerates", "skbio.sequence.GrammaredSequence.read", "skbio.sequence.GrammaredSequence.replace", "skbio.sequence.GrammaredSequence.to_definites", "skbio.sequence.GrammaredSequence.to_indices", "skbio.sequence.GrammaredSequence.to_regex", "skbio.sequence.GrammaredSequence.write", "skbio.sequence.Protein", "skbio.sequence.Protein.__bool__", "skbio.sequence.Protein.__contains__", "skbio.sequence.Protein.__copy__", "skbio.sequence.Protein.__deepcopy__", "skbio.sequence.Protein.__eq__", "skbio.sequence.Protein.__ge__", "skbio.sequence.Protein.__getitem__", "skbio.sequence.Protein.__getstate__", "skbio.sequence.Protein.__gt__", "skbio.sequence.Protein.__iter__", "skbio.sequence.Protein.__le__", "skbio.sequence.Protein.__len__", "skbio.sequence.Protein.__lt__", "skbio.sequence.Protein.__ne__", "skbio.sequence.Protein.__reversed__", "skbio.sequence.Protein.__str__", "skbio.sequence.Protein.concat", "skbio.sequence.Protein.count", "skbio.sequence.Protein.definites", "skbio.sequence.Protein.degap", "skbio.sequence.Protein.degenerates", "skbio.sequence.Protein.distance", "skbio.sequence.Protein.expand_degenerates", "skbio.sequence.Protein.find_motifs", "skbio.sequence.Protein.find_with_regex", "skbio.sequence.Protein.frequencies", "skbio.sequence.Protein.gaps", "skbio.sequence.Protein.has_definites", "skbio.sequence.Protein.has_degenerates", "skbio.sequence.Protein.has_gaps", "skbio.sequence.Protein.has_interval_metadata", "skbio.sequence.Protein.has_metadata", "skbio.sequence.Protein.has_nondegenerates", "skbio.sequence.Protein.has_positional_metadata", "skbio.sequence.Protein.has_stops", "skbio.sequence.Protein.index", "skbio.sequence.Protein.iter_contiguous", "skbio.sequence.Protein.iter_kmers", "skbio.sequence.Protein.kmer_frequencies", "skbio.sequence.Protein.lowercase", "skbio.sequence.Protein.match_frequency", "skbio.sequence.Protein.matches", "skbio.sequence.Protein.mismatch_frequency", "skbio.sequence.Protein.mismatches", "skbio.sequence.Protein.nondegenerates", "skbio.sequence.Protein.read", "skbio.sequence.Protein.replace", "skbio.sequence.Protein.stops", "skbio.sequence.Protein.to_definites", "skbio.sequence.Protein.to_indices", "skbio.sequence.Protein.to_regex", "skbio.sequence.Protein.write", "skbio.sequence.RNA", "skbio.sequence.RNA.__bool__", "skbio.sequence.RNA.__contains__", "skbio.sequence.RNA.__copy__", "skbio.sequence.RNA.__deepcopy__", "skbio.sequence.RNA.__eq__", "skbio.sequence.RNA.__ge__", "skbio.sequence.RNA.__getitem__", "skbio.sequence.RNA.__getstate__", "skbio.sequence.RNA.__gt__", "skbio.sequence.RNA.__iter__", "skbio.sequence.RNA.__le__", "skbio.sequence.RNA.__len__", "skbio.sequence.RNA.__lt__", "skbio.sequence.RNA.__ne__", "skbio.sequence.RNA.__reversed__", "skbio.sequence.RNA.__str__", "skbio.sequence.RNA.complement", "skbio.sequence.RNA.concat", "skbio.sequence.RNA.count", "skbio.sequence.RNA.definites", "skbio.sequence.RNA.degap", "skbio.sequence.RNA.degenerates", "skbio.sequence.RNA.distance", "skbio.sequence.RNA.expand_degenerates", "skbio.sequence.RNA.find_motifs", "skbio.sequence.RNA.find_with_regex", "skbio.sequence.RNA.frequencies", "skbio.sequence.RNA.gaps", "skbio.sequence.RNA.gc_content", "skbio.sequence.RNA.gc_frequency", "skbio.sequence.RNA.has_definites", "skbio.sequence.RNA.has_degenerates", "skbio.sequence.RNA.has_gaps", "skbio.sequence.RNA.has_interval_metadata", "skbio.sequence.RNA.has_metadata", "skbio.sequence.RNA.has_nondegenerates", "skbio.sequence.RNA.has_positional_metadata", "skbio.sequence.RNA.index", "skbio.sequence.RNA.is_reverse_complement", "skbio.sequence.RNA.iter_contiguous", "skbio.sequence.RNA.iter_kmers", "skbio.sequence.RNA.kmer_frequencies", "skbio.sequence.RNA.lowercase", "skbio.sequence.RNA.match_frequency", "skbio.sequence.RNA.matches", "skbio.sequence.RNA.mismatch_frequency", "skbio.sequence.RNA.mismatches", "skbio.sequence.RNA.nondegenerates", "skbio.sequence.RNA.read", "skbio.sequence.RNA.replace", "skbio.sequence.RNA.reverse_complement", "skbio.sequence.RNA.reverse_transcribe", "skbio.sequence.RNA.to_definites", "skbio.sequence.RNA.to_indices", "skbio.sequence.RNA.to_regex", "skbio.sequence.RNA.translate", "skbio.sequence.RNA.translate_six_frames", "skbio.sequence.RNA.write", "skbio.sequence.Sequence", "skbio.sequence.Sequence.__bool__", "skbio.sequence.Sequence.__contains__", "skbio.sequence.Sequence.__copy__", "skbio.sequence.Sequence.__deepcopy__", "skbio.sequence.Sequence.__eq__", "skbio.sequence.Sequence.__ge__", "skbio.sequence.Sequence.__getitem__", "skbio.sequence.Sequence.__getstate__", "skbio.sequence.Sequence.__gt__", "skbio.sequence.Sequence.__iter__", "skbio.sequence.Sequence.__le__", "skbio.sequence.Sequence.__len__", "skbio.sequence.Sequence.__lt__", "skbio.sequence.Sequence.__ne__", "skbio.sequence.Sequence.__reversed__", "skbio.sequence.Sequence.__str__", "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.has_interval_metadata", "skbio.sequence.Sequence.has_metadata", "skbio.sequence.Sequence.has_positional_metadata", "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.__contains__", "skbio.sequence.SubstitutionMatrix.__eq__", "skbio.sequence.SubstitutionMatrix.__ge__", "skbio.sequence.SubstitutionMatrix.__getitem__", "skbio.sequence.SubstitutionMatrix.__getstate__", "skbio.sequence.SubstitutionMatrix.__gt__", "skbio.sequence.SubstitutionMatrix.__le__", "skbio.sequence.SubstitutionMatrix.__lt__", "skbio.sequence.SubstitutionMatrix.__ne__", "skbio.sequence.SubstitutionMatrix.__str__", "skbio.sequence.SubstitutionMatrix.between", "skbio.sequence.SubstitutionMatrix.by_name", "skbio.sequence.SubstitutionMatrix.copy", "skbio.sequence.SubstitutionMatrix.filter", "skbio.sequence.SubstitutionMatrix.from_dict", "skbio.sequence.SubstitutionMatrix.from_iterable", "skbio.sequence.SubstitutionMatrix.get_names", "skbio.sequence.SubstitutionMatrix.identity", "skbio.sequence.SubstitutionMatrix.index", "skbio.sequence.SubstitutionMatrix.plot", "skbio.sequence.SubstitutionMatrix.read", "skbio.sequence.SubstitutionMatrix.redundant_form", "skbio.sequence.SubstitutionMatrix.to_data_frame", "skbio.sequence.SubstitutionMatrix.to_dict", "skbio.sequence.SubstitutionMatrix.transpose", "skbio.sequence.SubstitutionMatrix.within", "skbio.sequence.SubstitutionMatrix.write", "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 matrices and distance-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.__contains__", "skbio.stats.distance.DissimilarityMatrix.__eq__", "skbio.stats.distance.DissimilarityMatrix.__ge__", "skbio.stats.distance.DissimilarityMatrix.__getitem__", "skbio.stats.distance.DissimilarityMatrix.__getstate__", "skbio.stats.distance.DissimilarityMatrix.__gt__", "skbio.stats.distance.DissimilarityMatrix.__le__", "skbio.stats.distance.DissimilarityMatrix.__lt__", "skbio.stats.distance.DissimilarityMatrix.__ne__", "skbio.stats.distance.DissimilarityMatrix.__str__", "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.to_data_frame", "skbio.stats.distance.DissimilarityMatrix.transpose", "skbio.stats.distance.DissimilarityMatrix.within", "skbio.stats.distance.DissimilarityMatrix.write", "skbio.stats.distance.DissimilarityMatrixError", "skbio.stats.distance.DistanceMatrix", "skbio.stats.distance.DistanceMatrix.__contains__", "skbio.stats.distance.DistanceMatrix.__eq__", "skbio.stats.distance.DistanceMatrix.__ge__", "skbio.stats.distance.DistanceMatrix.__getitem__", "skbio.stats.distance.DistanceMatrix.__getstate__", "skbio.stats.distance.DistanceMatrix.__gt__", "skbio.stats.distance.DistanceMatrix.__le__", "skbio.stats.distance.DistanceMatrix.__lt__", "skbio.stats.distance.DistanceMatrix.__ne__", "skbio.stats.distance.DistanceMatrix.__str__", "skbio.stats.distance.DistanceMatrix.between", "skbio.stats.distance.DistanceMatrix.condensed_form", "skbio.stats.distance.DistanceMatrix.copy", "skbio.stats.distance.DistanceMatrix.filter", "skbio.stats.distance.DistanceMatrix.from_iterable", "skbio.stats.distance.DistanceMatrix.index", "skbio.stats.distance.DistanceMatrix.permute", "skbio.stats.distance.DistanceMatrix.plot", "skbio.stats.distance.DistanceMatrix.read", "skbio.stats.distance.DistanceMatrix.redundant_form", "skbio.stats.distance.DistanceMatrix.to_data_frame", "skbio.stats.distance.DistanceMatrix.to_series", "skbio.stats.distance.DistanceMatrix.transpose", "skbio.stats.distance.DistanceMatrix.within", "skbio.stats.distance.DistanceMatrix.write", "skbio.stats.distance.DistanceMatrixError", "skbio.stats.distance.MissingIDError", "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.AverageGradientANOVA.__eq__", "skbio.stats.gradient.AverageGradientANOVA.__ge__", "skbio.stats.gradient.AverageGradientANOVA.__getstate__", "skbio.stats.gradient.AverageGradientANOVA.__gt__", "skbio.stats.gradient.AverageGradientANOVA.__hash__", "skbio.stats.gradient.AverageGradientANOVA.__le__", "skbio.stats.gradient.AverageGradientANOVA.__lt__", "skbio.stats.gradient.AverageGradientANOVA.__ne__", "skbio.stats.gradient.AverageGradientANOVA.__str__", "skbio.stats.gradient.AverageGradientANOVA.get_trajectories", "skbio.stats.gradient.CategoryResults", "skbio.stats.gradient.CategoryResults.__eq__", "skbio.stats.gradient.CategoryResults.__ge__", "skbio.stats.gradient.CategoryResults.__getstate__", "skbio.stats.gradient.CategoryResults.__gt__", "skbio.stats.gradient.CategoryResults.__hash__", "skbio.stats.gradient.CategoryResults.__le__", "skbio.stats.gradient.CategoryResults.__lt__", "skbio.stats.gradient.CategoryResults.__ne__", "skbio.stats.gradient.CategoryResults.__str__", "skbio.stats.gradient.CategoryResults.to_files", "skbio.stats.gradient.FirstDifferenceGradientANOVA", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__eq__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__ge__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__getstate__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__gt__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__hash__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__le__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__lt__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__ne__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.__str__", "skbio.stats.gradient.FirstDifferenceGradientANOVA.get_trajectories", "skbio.stats.gradient.GradientANOVA", "skbio.stats.gradient.GradientANOVA.__eq__", "skbio.stats.gradient.GradientANOVA.__ge__", "skbio.stats.gradient.GradientANOVA.__getstate__", "skbio.stats.gradient.GradientANOVA.__gt__", "skbio.stats.gradient.GradientANOVA.__hash__", "skbio.stats.gradient.GradientANOVA.__le__", "skbio.stats.gradient.GradientANOVA.__lt__", "skbio.stats.gradient.GradientANOVA.__ne__", "skbio.stats.gradient.GradientANOVA.__str__", "skbio.stats.gradient.GradientANOVA.get_trajectories", "skbio.stats.gradient.GradientANOVAResults", "skbio.stats.gradient.GradientANOVAResults.__eq__", "skbio.stats.gradient.GradientANOVAResults.__ge__", "skbio.stats.gradient.GradientANOVAResults.__getstate__", "skbio.stats.gradient.GradientANOVAResults.__gt__", "skbio.stats.gradient.GradientANOVAResults.__hash__", "skbio.stats.gradient.GradientANOVAResults.__le__", "skbio.stats.gradient.GradientANOVAResults.__lt__", "skbio.stats.gradient.GradientANOVAResults.__ne__", "skbio.stats.gradient.GradientANOVAResults.__str__", "skbio.stats.gradient.GradientANOVAResults.to_files", "skbio.stats.gradient.GroupResults", "skbio.stats.gradient.GroupResults.__eq__", "skbio.stats.gradient.GroupResults.__ge__", "skbio.stats.gradient.GroupResults.__getstate__", "skbio.stats.gradient.GroupResults.__gt__", "skbio.stats.gradient.GroupResults.__hash__", "skbio.stats.gradient.GroupResults.__le__", "skbio.stats.gradient.GroupResults.__lt__", "skbio.stats.gradient.GroupResults.__ne__", "skbio.stats.gradient.GroupResults.__str__", "skbio.stats.gradient.GroupResults.to_files", "skbio.stats.gradient.TrajectoryGradientANOVA", "skbio.stats.gradient.TrajectoryGradientANOVA.__eq__", "skbio.stats.gradient.TrajectoryGradientANOVA.__ge__", "skbio.stats.gradient.TrajectoryGradientANOVA.__getstate__", "skbio.stats.gradient.TrajectoryGradientANOVA.__gt__", "skbio.stats.gradient.TrajectoryGradientANOVA.__hash__", "skbio.stats.gradient.TrajectoryGradientANOVA.__le__", "skbio.stats.gradient.TrajectoryGradientANOVA.__lt__", "skbio.stats.gradient.TrajectoryGradientANOVA.__ne__", "skbio.stats.gradient.TrajectoryGradientANOVA.__str__", "skbio.stats.gradient.TrajectoryGradientANOVA.get_trajectories", "skbio.stats.gradient.WindowDifferenceGradientANOVA", "skbio.stats.gradient.WindowDifferenceGradientANOVA.__eq__", "skbio.stats.gradient.WindowDifferenceGradientANOVA.__ge__", "skbio.stats.gradient.WindowDifferenceGradientANOVA.__getstate__", "skbio.stats.gradient.WindowDifferenceGradientANOVA.__gt__", "skbio.stats.gradient.WindowDifferenceGradientANOVA.__hash__", "skbio.stats.gradient.WindowDifferenceGradientANOVA.__le__", "skbio.stats.gradient.WindowDifferenceGradientANOVA.__lt__", "skbio.stats.gradient.WindowDifferenceGradientANOVA.__ne__", "skbio.stats.gradient.WindowDifferenceGradientANOVA.__str__", "skbio.stats.gradient.WindowDifferenceGradientANOVA.get_trajectories", "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.__eq__", "skbio.stats.ordination.OrdinationResults.__ge__", "skbio.stats.ordination.OrdinationResults.__getstate__", "skbio.stats.ordination.OrdinationResults.__gt__", "skbio.stats.ordination.OrdinationResults.__hash__", "skbio.stats.ordination.OrdinationResults.__le__", "skbio.stats.ordination.OrdinationResults.__lt__", "skbio.stats.ordination.OrdinationResults.__ne__", "skbio.stats.ordination.OrdinationResults.__str__", "skbio.stats.ordination.OrdinationResults.plot", "skbio.stats.ordination.OrdinationResults.read", "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.tree.DuplicateNodeError", "skbio.tree.MissingNodeError", "skbio.tree.NoLengthError", "skbio.tree.NoParentError", "skbio.tree.TreeError", "skbio.tree.TreeNode", "skbio.tree.TreeNode.__copy__", "skbio.tree.TreeNode.__deepcopy__", "skbio.tree.TreeNode.__eq__", "skbio.tree.TreeNode.__ge__", "skbio.tree.TreeNode.__getitem__", "skbio.tree.TreeNode.__getstate__", "skbio.tree.TreeNode.__gt__", "skbio.tree.TreeNode.__hash__", "skbio.tree.TreeNode.__iter__", "skbio.tree.TreeNode.__le__", "skbio.tree.TreeNode.__len__", "skbio.tree.TreeNode.__lt__", "skbio.tree.TreeNode.__ne__", "skbio.tree.TreeNode.__str__", "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.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_children", "skbio.tree.TreeNode.index_tree", "skbio.tree.TreeNode.invalidate_caches", "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", 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700, 709, 735, 749, 806, 807, 875, 876], "target_sequ": [0, 2, 16, 17], "gctaactaggctcccttctacccctctcagaga": 0, "gcccagtagcttcccaatatgagagcatcaattgtagatcgggcc": 0, "tctataagattccgcatgcgttacttataagatgtctcaacgg": 0, "tagagattaattgccactgccaaaattctg": 0, "query_sequ": [0, 2, 16, 17], "append": [0, 48, 144, 149, 457, 767], "act": [0, 54, 161, 162, 163], "aggctc": 0, "38": [0, 133, 138, 143, 724], "aligned_query_sequ": [0, 2], "tctacccctctcagaga": 0, "aligned_target_sequ": [0, 2], "aggctcccttctacccctctcagaga": 0, "scikit": [0, 1, 51, 52, 55, 59, 60, 63, 66, 67, 78, 105, 106, 107, 108, 109, 110, 111, 132, 133, 134, 135, 136, 137, 138, 142, 143, 144, 145, 147, 148, 220, 222, 258, 260, 272, 279, 280, 281, 282, 292, 293, 326, 328, 339, 344, 377, 379, 391, 397, 433, 435, 447, 454, 455, 456, 480, 481, 491, 494, 516, 522, 523, 565, 570, 591, 597, 711, 712, 792, 813, 816, 878, 881], "bio": [0, 1, 51, 52, 55, 59, 60, 63, 66, 67, 78, 105, 106, 107, 108, 109, 110, 111, 132, 133, 134, 135, 136, 137, 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600, 601, 602, 603, 604, 605, 606, 608, 643, 687, 698, 714, 718, 719, 721, 722, 724, 725, 727, 728, 729, 755, 762, 799, 818, 819], "observ": [1, 78, 81, 90, 93, 101, 105, 106, 111, 132, 223, 250, 276, 294, 320, 342, 345, 371, 395, 398, 425, 452, 457, 478, 493, 529, 608, 699, 724, 727, 728, 786, 814, 882], "particular": [1, 735, 817, 882], "associ": [1, 35, 69, 94, 138, 146, 147, 148, 151, 176, 177, 178, 194, 215, 217, 219, 223, 345, 398, 457, 601, 608, 698, 718, 722, 725, 726, 727, 765, 771, 804, 876], "throughout": [1, 141, 282, 291, 727, 881], "array_lik": [1, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 107, 108, 111, 230, 248, 249, 263, 273, 301, 318, 319, 330, 340, 352, 369, 370, 382, 392, 405, 423, 424, 438, 448, 464, 477, 483, 492, 527, 528, 530, 531, 532, 533, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 546, 548, 600, 602, 603, 604, 605, 608, 715, 718, 722, 725, 728, 729], "anyth": [1, 137, 138, 145, 149, 457, 841, 852, 864, 882], "convert": [1, 133, 135, 136, 137, 139, 142, 144, 147, 191, 223, 246, 275, 276, 316, 341, 342, 345, 367, 394, 395, 398, 421, 451, 452, 457, 476, 493, 548, 589, 601, 729, 755, 820], "d": [1, 16, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 105, 106, 107, 133, 134, 139, 142, 143, 223, 345, 398, 506, 510, 515, 521, 526, 527, 528, 529, 532, 533, 535, 536, 537, 540, 541, 542, 543, 544, 545, 546, 547, 559, 564, 569, 583, 590, 594, 596, 600, 601, 602, 603, 604, 608, 643, 665, 687, 700, 710, 718, 727, 728, 729, 736, 737, 750, 751, 753, 755, 756, 757, 758, 759, 761, 762, 764, 765, 766, 768, 769, 770, 771, 775, 781, 782, 783, 784, 785, 791, 795, 796, 797, 799, 800, 801, 802, 804, 805, 806, 809, 810, 811, 812, 814, 815, 876, 878, 880, 882], "numpi": [1, 107, 499, 517, 527, 528, 530, 531, 532, 533, 535, 536, 537, 538, 540, 541, 542, 543, 544, 546, 547, 548, 552, 566, 576, 584, 592, 600, 604, 606, 608, 609, 643, 665, 687, 698, 699, 724, 726, 727, 728, 729, 760, 799, 878], "arrai": [1, 16, 47, 50, 78, 94, 105, 106, 137, 143, 223, 240, 243, 245, 251, 268, 270, 271, 274, 276, 294, 313, 315, 321, 335, 337, 338, 342, 345, 364, 366, 372, 387, 389, 390, 393, 395, 398, 415, 418, 420, 426, 443, 445, 446, 449, 452, 457, 488, 490, 493, 495, 497, 505, 510, 513, 517, 527, 528, 530, 531, 532, 533, 535, 536, 537, 538, 540, 541, 542, 543, 544, 545, 547, 548, 550, 558, 566, 572, 574, 582, 584, 592, 608, 609, 643, 665, 687, 699, 718, 722, 724, 725, 726, 727, 728, 729, 777, 806, 814, 878], "nativ": [1, 517, 566, 592, 719], "list": [1, 66, 78, 94, 105, 106, 109, 110, 133, 136, 138, 139, 140, 143, 146, 147, 148, 149, 161, 163, 179, 180, 191, 204, 273, 340, 392, 448, 457, 492, 505, 509, 512, 545, 547, 558, 561, 582, 586, 602, 604, 605, 621, 643, 654, 676, 709, 724, 726, 727, 728, 735, 751, 757, 765, 767, 769, 772, 781, 783, 784, 799, 800, 804, 806, 807, 814, 815, 876, 882], "result": [1, 2, 16, 17, 47, 49, 54, 60, 61, 62, 78, 79, 83, 103, 105, 106, 107, 111, 133, 134, 137, 146, 149, 191, 216, 223, 240, 241, 244, 274, 276, 311, 314, 342, 345, 362, 365, 395, 398, 415, 416, 419, 449, 452, 474, 493, 529, 534, 537, 538, 541, 587, 600, 602, 603, 604, 605, 606, 609, 620, 621, 631, 632, 642, 653, 654, 664, 665, 675, 676, 686, 697, 698, 699, 700, 709, 710, 713, 714, 719, 721, 724, 729, 768, 784, 798, 806, 807, 814, 815, 819, 876, 878, 882], "ident": [1, 133, 134, 142, 146, 499, 552, 572, 576, 608, 730, 760, 793, 880], "As": [1, 136, 139, 142, 146, 457, 517, 566, 592, 602, 604, 714, 768, 876, 882], "mention": [1, 142], "which": [1, 2, 28, 60, 61, 62, 69, 74, 78, 88, 94, 98, 101, 105, 106, 108, 133, 135, 137, 139, 140, 141, 142, 143, 144, 146, 147, 148, 149, 151, 161, 162, 163, 164, 176, 178, 179, 180, 181, 182, 187, 223, 241, 242, 253, 261, 263, 266, 276, 292, 294, 311, 312, 329, 330, 333, 342, 345, 362, 363, 381, 382, 385, 395, 398, 416, 417, 428, 436, 438, 441, 452, 457, 474, 475, 482, 483, 486, 493, 506, 526, 527, 528, 529, 534, 548, 559, 583, 600, 603, 604, 608, 714, 718, 719, 724, 725, 726, 727, 728, 760, 763, 794, 795, 806, 807, 812, 814, 815, 825, 842, 864, 876, 878, 880, 882], "row": [1, 28, 103, 107, 108, 111, 131, 132, 144, 194, 495, 499, 514, 528, 529, 531, 534, 535, 536, 538, 539, 541, 542, 543, 544, 547, 548, 552, 563, 576, 588, 589, 594, 600, 601, 602, 603, 604, 605, 606, 608, 700, 713, 714, 717, 721, 727, 728, 818], "so": [1, 2, 47, 60, 61, 62, 63, 64, 65, 67, 78, 103, 105, 106, 107, 137, 142, 146, 149, 191, 192, 204, 207, 252, 253, 427, 428, 602, 676, 699, 713, 714, 715, 719, 721, 724, 726, 727, 728, 814, 876, 880, 882], "column": [1, 16, 28, 52, 53, 54, 107, 131, 132, 137, 139, 140, 143, 144, 147, 148, 241, 260, 266, 311, 328, 333, 362, 379, 385, 416, 435, 441, 457, 474, 481, 486, 495, 499, 514, 518, 527, 528, 529, 534, 535, 536, 547, 552, 563, 567, 576, 588, 589, 593, 600, 601, 602, 603, 604, 605, 606, 608, 643, 687, 699, 710, 713, 714, 715, 717, 721, 722, 726, 727, 773, 777, 818, 819], "some": [1, 16, 68, 78, 80, 90, 94, 137, 139, 142, 145, 146, 161, 162, 163, 194, 218, 223, 345, 398, 528, 541, 542, 543, 714, 724, 727, 841, 880, 882], "incorpor": [1, 94, 525], "relationship": [1, 94, 142, 713, 714, 721, 724, 728, 815], "between": [1, 16, 61, 64, 74, 79, 80, 84, 95, 102, 105, 106, 107, 111, 131, 137, 138, 139, 141, 144, 147, 148, 207, 221, 241, 246, 267, 268, 269, 270, 311, 316, 334, 335, 336, 337, 362, 367, 386, 387, 388, 389, 416, 421, 442, 443, 444, 445, 474, 476, 487, 488, 489, 490, 495, 499, 511, 523, 524, 525, 529, 534, 544, 547, 548, 552, 562, 572, 576, 587, 600, 601, 602, 603, 604, 605, 607, 608, 643, 713, 714, 715, 721, 724, 727, 728, 735, 750, 758, 759, 760, 766, 775, 785, 804, 805, 815, 878, 880], "through": [1, 35, 60, 61, 62, 146, 175, 181, 186, 499, 552, 576, 719, 768, 882], "phylogenet": [1, 78, 94, 105, 106, 142, 144, 547, 608, 735, 758, 768, 815, 875, 878], "tree": 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480, 486, 492, 498, 501, 502, 503, 506, 521, 526, 529, 531, 534, 538, 539, 540, 541, 542, 543, 546, 551, 554, 555, 556, 559, 569, 575, 578, 579, 580, 583, 596, 600, 601, 602, 603, 604, 605, 606, 608, 611, 612, 614, 616, 617, 618, 622, 623, 625, 627, 628, 629, 631, 633, 634, 636, 638, 639, 640, 643, 644, 645, 647, 649, 650, 651, 655, 656, 658, 660, 661, 662, 664, 666, 667, 669, 671, 672, 673, 675, 677, 678, 680, 682, 683, 684, 688, 689, 691, 693, 694, 695, 698, 701, 702, 704, 706, 707, 708, 710, 713, 714, 718, 719, 721, 723, 724, 725, 726, 727, 728, 735, 738, 739, 742, 745, 747, 748, 755, 757, 760, 799, 806, 817, 818, 819, 823, 824, 827, 829, 830, 831, 832, 841, 843, 844, 846, 848, 849, 850, 853, 855, 856, 858, 860, 861, 862, 864, 866, 867, 869, 871, 872, 873, 882], "tip": [1, 78, 94, 105, 106, 735, 753, 755, 757, 758, 759, 760, 762, 763, 765, 766, 768, 775, 780, 781, 782, 783, 785, 786, 788, 789, 790, 796, 797, 798, 799, 801, 802, 804, 807, 808, 809, 814, 876, 880], "optim": [1, 2, 16, 79, 103, 105, 106, 107, 604, 766, 816, 875], "time": [1, 16, 45, 48, 78, 90, 99, 105, 106, 108, 137, 138, 146, 495, 535, 536, 544, 584, 600, 601, 602, 603, 605, 609, 632, 687, 721, 724, 727, 728, 735, 799, 882], "often": [1, 78, 103, 107, 136, 137, 139, 547, 608, 714, 719, 724, 839], "faster": [1, 78, 105, 106, 108, 250, 280, 293, 320, 371, 425, 455, 478, 604, 719, 788], "repeat": [1, 138, 724, 838], "call": [1, 54, 78, 79, 84, 85, 105, 106, 135, 137, 144, 147, 149, 191, 194, 241, 249, 252, 273, 292, 311, 319, 340, 362, 370, 392, 416, 424, 427, 448, 457, 474, 477, 492, 589, 601, 602, 698, 714, 724, 751, 753, 754, 757, 768, 769, 771, 784, 785, 791, 800, 805, 812, 839, 841, 842, 852, 876, 882], "reason": [1, 79, 90, 136, 142, 727, 755], "matric": [1, 62, 65, 131, 141, 345, 495, 497, 504, 507, 512, 548, 550, 557, 574, 581, 601, 602, 605, 607, 608, 715, 719, 760], "rather": [1, 83, 142, 495, 526, 608, 815], "thu": [1, 137, 138, 142, 146, 250, 320, 371, 425, 457, 478, 499, 552, 572, 576, 600, 602, 604, 608, 719], "slow": [1, 78, 103, 105, 106, 107, 875], "possibl": [1, 16, 35, 95, 99, 137, 138, 146, 147, 218, 247, 280, 282, 293, 317, 368, 422, 455, 601, 605, 727, 760, 808, 814], "disabl": [1, 78, 103, 105, 106, 107, 882], "step": [1, 28, 45, 48, 56, 78, 103, 105, 106, 107, 144, 149, 717, 724], "pass": [1, 28, 35, 48, 55, 56, 59, 66, 103, 107, 108, 109, 110, 133, 135, 137, 139, 144, 145, 147, 161, 162, 163, 175, 181, 182, 183, 184, 186, 187, 188, 189, 191, 220, 222, 223, 246, 248, 250, 272, 273, 281, 292, 316, 318, 320, 339, 340, 344, 345, 367, 369, 371, 391, 392, 397, 398, 421, 423, 425, 447, 448, 456, 457, 476, 478, 491, 492, 494, 499, 516, 522, 552, 565, 570, 576, 587, 589, 591, 597, 602, 605, 643, 711, 712, 727, 781, 783, 792, 813, 815, 864, 880, 882], "fals": [1, 14, 15, 16, 29, 30, 31, 32, 33, 45, 46, 48, 50, 51, 52, 53, 57, 60, 61, 62, 72, 73, 78, 94, 103, 105, 106, 107, 133, 136, 137, 138, 139, 140, 142, 145, 161, 162, 163, 191, 192, 194, 204, 216, 217, 223, 224, 225, 226, 228, 230, 237, 240, 241, 243, 244, 245, 247, 250, 251, 253, 254, 255, 256, 258, 259, 260, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 273, 274, 275, 276, 277, 278, 279, 280, 282, 283, 292, 293, 294, 295, 296, 297, 299, 301, 308, 311, 313, 314, 315, 317, 320, 321, 322, 323, 324, 326, 327, 328, 330, 331, 332, 333, 334, 335, 336, 337, 338, 340, 341, 342, 343, 345, 346, 347, 348, 350, 352, 359, 362, 364, 365, 366, 368, 371, 372, 373, 374, 375, 377, 378, 379, 380, 382, 383, 384, 385, 386, 387, 388, 389, 390, 392, 393, 394, 395, 396, 398, 399, 400, 401, 403, 405, 412, 415, 416, 418, 419, 420, 422, 425, 426, 428, 429, 430, 431, 433, 434, 435, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 448, 449, 450, 451, 452, 453, 454, 455, 457, 458, 459, 460, 462, 464, 471, 474, 478, 480, 481, 483, 484, 485, 486, 487, 488, 489, 490, 492, 493, 496, 497, 504, 506, 529, 534, 540, 546, 549, 550, 557, 559, 573, 574, 581, 583, 587, 589, 602, 605, 608, 609, 610, 632, 643, 676, 719, 721, 724, 726, 727, 729, 753, 758, 759, 762, 770, 776, 779, 780, 785, 793, 805, 807, 808, 810, 819, 841, 864, 878, 880, 882], "danger": 1, "If": [1, 16, 28, 45, 47, 48, 50, 53, 54, 55, 56, 57, 58, 60, 61, 62, 64, 66, 69, 72, 73, 78, 79, 80, 84, 90, 94, 103, 105, 106, 107, 108, 111, 133, 137, 140, 141, 142, 143, 144, 145, 146, 147, 149, 151, 161, 162, 163, 176, 178, 182, 183, 187, 188, 191, 194, 203, 207, 220, 221, 223, 225, 230, 240, 241, 242, 244, 246, 248, 250, 253, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 272, 274, 276, 277, 292, 294, 296, 301, 311, 312, 314, 316, 318, 320, 329, 330, 331, 332, 333, 334, 335, 336, 337, 339, 342, 343, 345, 347, 352, 362, 363, 365, 367, 369, 371, 381, 382, 383, 384, 385, 386, 387, 388, 389, 391, 395, 396, 398, 400, 405, 415, 416, 417, 419, 421, 423, 425, 428, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 447, 449, 452, 453, 454, 455, 457, 459, 464, 474, 475, 476, 478, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 493, 499, 506, 507, 509, 510, 511, 514, 515, 516, 521, 524, 525, 529, 531, 534, 535, 536, 538, 539, 545, 548, 552, 559, 561, 562, 563, 564, 565, 569, 576, 583, 586, 587, 588, 589, 590, 591, 596, 600, 601, 602, 603, 604, 605, 606, 608, 643, 654, 687, 698, 709, 710, 711, 713, 714, 715, 718, 719, 722, 724, 725, 726, 727, 728, 729, 755, 757, 758, 762, 765, 768, 769, 773, 778, 781, 783, 786, 792, 797, 798, 799, 804, 806, 807, 808, 814, 815, 818, 819, 820, 821], "invalid": [1, 50, 54, 78, 94, 103, 105, 106, 107, 137, 223, 345, 398, 601, 602, 710, 752, 757, 767, 778, 787, 791], "encount": [1, 146, 766, 768, 775], "when": [1, 16, 45, 47, 48, 54, 57, 60, 61, 62, 69, 79, 94, 95, 99, 108, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 133, 135, 137, 138, 139, 140, 141, 142, 144, 145, 146, 147, 149, 150, 161, 162, 163, 182, 183, 184, 187, 188, 189, 191, 204, 216, 223, 241, 248, 249, 252, 253, 266, 294, 311, 318, 319, 333, 345, 362, 369, 370, 385, 398, 416, 423, 424, 427, 428, 441, 457, 474, 477, 486, 524, 529, 547, 600, 602, 603, 604, 606, 608, 631, 664, 675, 713, 721, 724, 725, 726, 727, 728, 729, 732, 760, 794, 811, 812, 815, 819, 820, 841, 876, 880, 882], "difficult": 1, "interpret": [1, 47, 74, 78, 103, 105, 106, 107, 131, 142, 146, 526, 713, 714, 721], "error": [1, 47, 78, 90, 94, 103, 105, 106, 107, 137, 138, 144, 146, 149, 191, 218, 276, 342, 395, 452, 493, 571, 598, 599, 600, 602, 604, 724, 728, 734, 820, 876], "messag": [1, 78, 103, 105, 106, 107, 621, 665, 820, 876], "incorrect": 1, "recommend": [1, 83, 94, 144, 147, 223, 294, 345, 398, 457, 529, 547, 710, 713, 721, 727], "user": [1, 47, 104, 112, 133, 146, 148, 149, 151, 161, 162, 163, 182, 184, 187, 189, 275, 341, 394, 451, 529, 534, 714, 719, 816, 875, 878], "care": [1, 47, 137, 139, 604], "ensur": [1, 16, 47, 78, 105, 106, 149, 223, 345, 398, 497, 531, 534, 538, 550, 572, 574, 756, 818], "data": [1, 28, 54, 78, 80, 90, 94, 103, 105, 106, 107, 108, 111, 132, 133, 136, 138, 140, 141, 143, 145, 146, 147, 148, 191, 223, 294, 345, 398, 457, 495, 497, 499, 517, 526, 527, 528, 529, 530, 533, 534, 536, 538, 540, 544, 546, 548, 550, 552, 566, 572, 574, 576, 592, 601, 608, 609, 631, 664, 675, 698, 710, 713, 714, 718, 724, 726, 727, 728, 773, 804, 808, 815, 839, 842, 875, 876, 878, 882], "condit": [1, 84, 85, 727], "follow": [1, 51, 52, 54, 66, 73, 78, 79, 94, 105, 106, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 194, 223, 230, 258, 260, 301, 326, 328, 345, 352, 377, 379, 398, 405, 433, 435, 457, 464, 480, 481, 499, 507, 527, 528, 529, 532, 533, 535, 536, 537, 541, 543, 544, 547, 552, 576, 600, 601, 602, 604, 605, 609, 710, 713, 728, 754, 791, 842, 880, 882], "confid": [1, 68, 73, 77, 84, 534, 724, 725, 735, 755], "met": [1, 345, 864], "safe": [1, 78, 103, 105, 106, 107, 146, 719, 729, 753], "cast": [1, 142, 241, 311, 362, 416, 474, 547, 548, 606, 710], "integ": [1, 16, 103, 107, 131, 133, 137, 138, 141, 142, 143, 144, 145, 230, 301, 352, 405, 464, 529, 534, 547, 548, 600, 603, 604, 605, 606, 687, 729], "neg": [1, 16, 61, 64, 67, 80, 146, 292, 531, 538, 539, 572, 713, 714, 719, 724, 728, 815], "dimension": [1, 517, 528, 541, 542, 543, 548, 566, 584, 592, 713, 720, 721, 727, 728], "equal": [1, 33, 42, 47, 67, 69, 101, 105, 106, 107, 137, 195, 201, 207, 213, 228, 237, 283, 289, 299, 308, 350, 359, 403, 412, 457, 462, 471, 495, 497, 504, 524, 541, 550, 557, 574, 581, 600, 602, 603, 604, 606, 608, 698, 713, 718, 719, 722, 727, 728, 729, 758, 814, 818, 819], "being": [1, 16, 45, 47, 48, 60, 61, 62, 78, 103, 107, 137, 138, 144, 148, 544, 604, 608, 698, 727, 736, 737, 757, 761, 764, 797, 876, 878], "confirm": [1, 119, 600, 604, 728], "uniqu": [1, 54, 58, 133, 137, 141, 142, 146, 147, 148, 276, 342, 395, 452, 493, 525, 547, 604, 710, 754, 763, 768], "root": [1, 78, 89, 94, 105, 106, 142, 148, 545, 736, 737, 750, 751, 752, 753, 755, 756, 757, 761, 764, 765, 766, 767, 770, 771, 773, 775, 779, 781, 783, 784, 791, 796, 797, 800, 802, 804, 806, 807, 809, 811, 812, 814, 815, 880], "ha": [1, 16, 28, 46, 51, 52, 60, 61, 62, 67, 111, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 183, 188, 191, 223, 240, 241, 244, 247, 257, 258, 259, 260, 271, 274, 278, 279, 280, 282, 292, 293, 294, 311, 314, 317, 325, 326, 327, 328, 338, 345, 362, 365, 368, 376, 377, 378, 379, 390, 398, 415, 416, 419, 422, 432, 433, 434, 435, 446, 449, 450, 454, 455, 457, 474, 479, 480, 481, 529, 531, 547, 698, 713, 715, 726, 727, 728, 756, 776, 779, 780, 794, 798, 814, 841, 878, 880], "node": [1, 78, 105, 106, 545, 730, 731, 735, 736, 737, 740, 744, 750, 751, 752, 754, 755, 756, 757, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771, 773, 775, 776, 777, 779, 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791, 793, 794, 796, 797, 800, 801, 804, 805, 806, 807, 808, 809, 810, 814, 876, 880], "except": [1, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 137, 142, 143, 144, 146, 150, 162, 185, 292, 509, 561, 571, 586, 598, 599, 603, 714, 730, 731, 732, 733, 734, 763, 814, 816, 817, 852, 875, 881], "branch": [1, 78, 94, 106, 545, 735, 755, 756, 765, 806, 809, 815, 880], "name": [1, 55, 59, 78, 94, 105, 106, 133, 134, 138, 139, 140, 142, 143, 145, 146, 147, 149, 151, 176, 177, 178, 183, 188, 194, 220, 222, 266, 272, 281, 282, 283, 289, 291, 333, 339, 344, 385, 391, 397, 441, 447, 456, 486, 491, 494, 495, 507, 512, 516, 522, 529, 534, 540, 545, 565, 570, 591, 597, 600, 601, 603, 604, 609, 621, 665, 700, 710, 711, 712, 730, 735, 749, 751, 752, 753, 755, 757, 758, 759, 760, 763, 767, 768, 769, 770, 771, 773, 775, 781, 782, 783, 784, 785, 786, 788, 789, 790, 791, 792, 794, 797, 798, 799, 800, 801, 802, 804, 805, 806, 807, 808, 813, 814, 833, 839, 876, 880], "correspond": [1, 53, 78, 94, 105, 106, 137, 138, 140, 145, 147, 183, 188, 253, 266, 282, 292, 333, 385, 428, 441, 454, 455, 486, 499, 529, 544, 552, 576, 699, 700, 713, 714, 717, 728, 735, 768, 773, 777, 786, 807, 814], "There": [1, 54, 79, 90, 134, 139, 142, 145, 247, 317, 368, 422, 572, 719, 727, 728, 876, 880, 882], "ecolog": [1, 76, 714, 719], "literatur": [1, 74, 728], "softwar": [1, 137, 138, 146, 875], "measur": [1, 74, 76, 82, 84, 85, 88, 89, 93, 94, 95, 97, 98, 99, 105, 106, 495, 529, 540, 546, 547, 713, 726, 727, 735, 755], "alwai": [1, 16, 136, 139, 142, 144, 146, 162, 191, 194, 215, 292, 765, 821, 882], "assum": [1, 69, 78, 80, 86, 89, 105, 106, 135, 137, 138, 141, 143, 161, 163, 230, 278, 279, 280, 301, 352, 405, 464, 499, 534, 547, 548, 552, 576, 587, 608, 609, 714, 718, 724, 725, 727, 728], "abund": [1, 69, 70, 78, 80, 83, 90, 94, 102, 103, 105, 106, 107, 108, 111, 132, 529, 534, 699, 713, 714, 720, 721, 728], "where": [1, 2, 67, 69, 70, 71, 72, 74, 76, 77, 78, 79, 80, 81, 82, 83, 86, 87, 88, 89, 90, 94, 95, 96, 97, 98, 99, 102, 107, 108, 111, 131, 137, 141, 142, 143, 146, 147, 149, 243, 245, 249, 251, 261, 263, 268, 270, 271, 273, 313, 315, 319, 321, 329, 330, 335, 337, 338, 340, 364, 366, 370, 372, 381, 382, 387, 389, 390, 392, 393, 418, 420, 424, 426, 436, 438, 443, 445, 446, 448, 477, 482, 483, 488, 490, 492, 495, 499, 527, 528, 529, 531, 532, 533, 534, 535, 536, 538, 539, 541, 542, 543, 544, 552, 576, 602, 608, 698, 710, 718, 720, 721, 722, 724, 728, 729, 735, 759, 760, 770, 774, 807, 810, 839, 880, 882], "three": [1, 28, 93, 144, 148, 541, 547, 572, 605, 699, 710, 727, 728, 760, 882], "were": [1, 62, 65, 78, 83, 103, 105, 106, 107, 142, 144, 145, 228, 263, 299, 330, 350, 382, 403, 438, 462, 483, 600, 602, 604, 710, 727, 728, 781, 783, 817, 882], "onli": [1, 16, 54, 81, 84, 94, 111, 135, 136, 137, 138, 139, 141, 142, 143, 144, 146, 147, 148, 149, 191, 204, 219, 223, 241, 248, 282, 311, 318, 345, 362, 369, 398, 416, 423, 457, 474, 495, 509, 526, 529, 541, 561, 572, 586, 587, 589, 594, 600, 604, 605, 698, 714, 719, 721, 726, 727, 728, 756, 759, 760, 762, 765, 768, 791, 799, 804, 808, 821, 864, 875, 880, 882], "second": [1, 16, 28, 60, 61, 62, 63, 64, 65, 66, 138, 144, 149, 163, 194, 216, 283, 499, 529, 552, 576, 728, 774, 777, 807, 876, 882], "form": [1, 28, 60, 193, 499, 548, 552, 572, 576, 594, 806], "among": [1, 74, 94, 139, 521, 569, 596, 610, 714, 721], "expect": [1, 108, 133, 149, 178, 185, 223, 345, 398, 534, 535, 536, 547, 608, 713, 714, 721, 731, 732, 806, 882], "3": [1, 16, 28, 33, 45, 46, 48, 50, 53, 54, 56, 57, 60, 64, 69, 77, 78, 81, 86, 94, 97, 102, 105, 106, 132, 133, 134, 135, 136, 137, 138, 139, 140, 142, 143, 144, 145, 146, 147, 148, 194, 204, 216, 221, 228, 230, 240, 241, 242, 247, 248, 264, 265, 267, 273, 274, 276, 279, 280, 292, 293, 299, 301, 311, 312, 317, 318, 331, 332, 334, 340, 342, 345, 350, 352, 362, 363, 368, 369, 383, 384, 386, 392, 395, 403, 405, 415, 416, 417, 422, 423, 439, 440, 442, 448, 449, 452, 454, 455, 457, 462, 464, 474, 475, 484, 485, 487, 492, 493, 506, 515, 518, 521, 525, 526, 527, 528, 530, 532, 533, 534, 535, 536, 537, 540, 541, 542, 543, 546, 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438, 441, 452, 457, 474, 478, 483, 486, 493, 507, 515, 521, 526, 538, 564, 569, 590, 596, 608, 698, 719, 721, 724, 726, 727, 728, 736, 737, 752, 754, 757, 761, 764, 765, 767, 787, 801, 802, 814, 821, 832, 833, 838, 878, 882], "alig": 15, "stripe": [16, 66], "band": 16, "must": [16, 28, 45, 48, 54, 55, 59, 78, 80, 94, 105, 106, 107, 108, 111, 133, 135, 137, 138, 141, 142, 143, 144, 146, 147, 162, 219, 220, 222, 223, 241, 246, 266, 272, 279, 281, 311, 316, 333, 339, 344, 345, 362, 367, 385, 391, 397, 398, 416, 421, 441, 447, 454, 456, 457, 474, 476, 486, 491, 494, 509, 516, 522, 529, 534, 545, 548, 561, 565, 570, 586, 591, 597, 600, 601, 602, 603, 604, 606, 608, 631, 664, 675, 698, 710, 711, 712, 713, 718, 727, 728, 729, 757, 792, 799, 807, 813, 814, 815, 818, 820, 840, 841, 864, 882], "instanti": [16, 136, 149, 294, 882], "callabl": [16, 28, 45, 48, 56, 103, 107, 108, 111, 511, 529, 562, 587], "reus": [16, 723], "larg": [16, 79, 83, 105, 106, 131, 137, 144, 538, 539, 601, 721, 727, 753, 760], "collect": [16, 95, 99, 101, 191, 506, 544, 559, 583, 698], "upper": [16, 83, 84, 137, 144, 194, 204, 216, 218, 587, 594, 602], "lowercas": [16, 136, 137, 138, 139, 145, 223, 241, 294, 311, 345, 362, 398, 416, 457, 474], "q": [16, 83, 134, 345, 714, 715], "h": [16, 69, 70, 74, 82, 94, 95, 96, 97, 98, 99, 137, 144, 147, 192, 223, 345, 398, 756, 757, 762, 765, 796, 797, 798, 801, 802, 811, 812, 814, 880], "l": [16, 70, 71, 78, 83, 84, 94, 102, 136, 138, 148, 292, 345, 544, 602, 699, 713, 714, 721, 807], "k": [16, 69, 74, 94, 95, 97, 98, 99, 108, 223, 250, 264, 265, 320, 331, 332, 345, 371, 383, 384, 398, 425, 439, 440, 478, 484, 485, 495, 507, 525, 544, 601, 608, 765, 799, 806, 814], "m": [16, 63, 69, 78, 94, 105, 106, 133, 134, 136, 138, 144, 148, 223, 282, 283, 292, 345, 398, 507, 601, 604, 608, 710, 713, 714, 720, 721, 723, 726, 798, 815], "w": [16, 47, 69, 70, 77, 90, 94, 102, 133, 134, 135, 191, 223, 345, 398, 529, 544], "y": [16, 69, 80, 138, 145, 223, 345, 398, 537, 541, 542, 546, 602, 605, 608, 699, 710, 714, 715, 720, 721, 726, 760, 806], "v": [16, 105, 106, 223, 228, 237, 299, 308, 345, 350, 359, 398, 403, 412, 462, 471, 526, 540, 544, 546, 726, 727, 806], "z": [16, 54, 77, 146, 345, 605, 710, 760, 806], "x": [16, 80, 96, 132, 138, 145, 276, 294, 342, 345, 395, 452, 493, 526, 527, 528, 530, 531, 532, 533, 535, 536, 537, 538, 541, 542, 543, 544, 546, 602, 605, 608, 699, 700, 710, 713, 714, 715, 721, 724, 727, 728, 760, 770, 791, 794, 806, 810, 815, 840, 882], "gap_open_penalti": [16, 60, 61, 62, 63, 64, 65], "int": [16, 40, 50, 57, 60, 61, 62, 63, 64, 65, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 107, 108, 111, 133, 139, 140, 145, 162, 191, 194, 204, 215, 219, 230, 235, 242, 248, 249, 253, 261, 263, 264, 265, 267, 269, 273, 291, 301, 306, 312, 318, 319, 329, 330, 331, 332, 334, 336, 340, 352, 357, 363, 369, 370, 381, 382, 383, 384, 386, 388, 392, 405, 410, 417, 423, 424, 428, 436, 438, 439, 440, 442, 444, 448, 454, 455, 464, 469, 475, 477, 482, 483, 484, 485, 487, 489, 492, 513, 514, 525, 527, 528, 534, 540, 546, 563, 588, 600, 602, 603, 604, 605, 606, 608, 643, 687, 698, 710, 714, 718, 719, 721, 722, 725, 727, 728, 729, 735, 756, 760, 762, 771, 777, 786, 787, 799, 814, 819, 820, 840, 853], "option": [16, 28, 45, 47, 48, 50, 53, 54, 55, 56, 57, 59, 60, 61, 62, 64, 65, 66, 67, 69, 72, 73, 78, 83, 84, 85, 90, 94, 97, 103, 105, 106, 107, 108, 111, 135, 137, 138, 143, 144, 146, 147, 148, 151, 161, 162, 163, 182, 183, 184, 187, 188, 189, 191, 194, 204, 215, 219, 220, 221, 222, 223, 228, 240, 241, 242, 246, 248, 249, 250, 253, 261, 263, 264, 265, 267, 269, 272, 275, 276, 281, 282, 291, 292, 293, 299, 311, 312, 316, 318, 319, 320, 329, 330, 331, 332, 334, 336, 339, 341, 342, 344, 345, 350, 362, 363, 367, 369, 370, 371, 381, 382, 383, 384, 386, 388, 391, 394, 395, 397, 398, 403, 415, 416, 417, 421, 423, 424, 425, 428, 436, 438, 439, 440, 442, 444, 447, 451, 452, 454, 455, 456, 457, 462, 474, 475, 476, 477, 478, 482, 483, 484, 485, 487, 489, 491, 493, 494, 506, 509, 511, 515, 516, 522, 525, 529, 534, 535, 536, 538, 539, 548, 559, 561, 562, 564, 565, 570, 583, 586, 587, 589, 590, 591, 597, 600, 601, 602, 603, 604, 605, 606, 608, 643, 698, 710, 711, 712, 714, 715, 718, 719, 721, 722, 725, 726, 727, 728, 729, 735, 756, 773, 778, 792, 799, 806, 807, 813, 814, 815, 818, 819, 840, 841, 842, 864, 878, 882], "cannot": [16, 28, 45, 48, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 137, 138, 141, 142, 146, 182, 183, 187, 188, 191, 241, 294, 311, 362, 416, 474, 529, 600, 601, 602, 603, 604, 698, 710, 726, 728, 729, 768, 771, 799, 876], "gap_extend_penalti": [16, 60, 61, 62, 63, 64, 65], "score_s": 16, "your": [16, 54, 78, 103, 105, 106, 107, 138, 146, 149, 204, 604, 724, 727, 876, 880, 882], "estim": [16, 69, 72, 73, 77, 79, 81, 83, 84, 85, 90, 96, 534, 718, 726, 727, 728], "best": [16, 60, 61, 62, 63, 64, 65, 84, 85, 526, 601, 713, 817], "255": [16, 714], "mask_length": 16, "suggest": [16, 162, 182, 183, 187, 188, 727], "len": [16, 28, 40, 235, 306, 357, 410, 469, 507, 606, 728, 736, 737, 761, 764, 802, 814, 882], "special": [16, 141, 149], "concern": [16, 141], "detail": [16, 53, 54, 66, 67, 94, 108, 110, 111, 136, 137, 138, 139, 140, 144, 145, 147, 148, 149, 293, 457, 499, 552, 576, 601, 605, 710, 713, 714, 721, 815, 876], "descript": [16, 69, 78, 83, 88, 89, 99, 103, 105, 106, 107, 131, 133, 137, 138, 139, 140, 142, 144, 146, 148, 499, 552, 576, 758, 814, 878, 880], "after": [16, 45, 48, 60, 61, 62, 137, 138, 146, 147, 148, 149, 207, 218, 534, 540, 541, 601, 602, 605, 608, 713, 728, 789, 791, 808], "locat": [16, 55, 59, 136, 142, 147, 176, 177, 178, 194, 220, 222, 248, 249, 272, 281, 318, 319, 339, 344, 369, 370, 391, 397, 423, 424, 447, 456, 477, 491, 494, 516, 522, 565, 570, 591, 597, 711, 712, 792, 796, 813, 818, 881], "heurist": [16, 604, 719], "found": [16, 101, 132, 134, 136, 137, 138, 139, 142, 144, 147, 182, 184, 187, 189, 276, 342, 395, 452, 493, 509, 561, 586, 601, 602, 604, 728, 758, 768, 769, 770, 771, 781, 783, 799, 814], "check": [16, 138, 162, 182, 187, 195, 204, 207, 218, 496, 497, 535, 536, 547, 548, 549, 550, 572, 573, 574, 609, 713, 714, 727, 818, 819, 839, 882], "largest": [16, 102], "maxim": [16, 94, 601, 714], "sw": [16, 726], "avoid": [16, 146, 147, 149, 218, 699, 722, 811, 812], "pick": [16, 727], "belong": [16, 70, 74, 140, 529, 534, 600, 603, 604], "share": [16, 51, 52, 54, 69, 241, 258, 260, 311, 326, 328, 362, 377, 379, 416, 433, 435, 457, 474, 480, 481, 880], "partial": [16, 94, 218], "librari": [16, 66, 105, 106, 137, 875, 876], "mask": [16, 276, 342, 395, 452, 493, 540, 546], "loci": 16, "nearbi": 16, "unmask": 16, "element": [16, 141, 191, 495, 499, 511, 531, 535, 536, 548, 552, 562, 572, 576, 587, 687, 710, 713, 717, 718, 722, 725, 727, 728, 729, 838], "15": [16, 62, 65, 83, 134, 143, 146, 609, 724, 727, 728, 804], "mask_auto": 16, "automat": [16, 45, 48, 54, 55, 59, 141, 145, 146, 175, 186, 194, 220, 222, 266, 272, 281, 333, 339, 344, 385, 391, 397, 441, 447, 456, 486, 491, 494, 516, 522, 547, 565, 570, 591, 597, 700, 711, 712, 760, 792, 813, 876], "max": [16, 69, 70, 90, 727, 728, 775], "score_onli": 16, "prevent": 16, "babp": 16, "overrid": [16, 61, 64, 94, 151, 161, 162, 163, 182, 187, 791, 882], "score_filt": 16, "distance_filt": 16, "override_skip_babp": 16, "highest": [16, 142], "preced": [16, 135, 142, 144], "less": [16, 69, 78, 85, 105, 106, 108, 144, 146, 264, 265, 331, 332, 383, 384, 439, 440, 484, 485, 525, 602, 605, 698, 713, 729, 786, 820], "save": [16, 204, 548, 631, 664, 675, 788], "computation": 16, "filter": [16, 47, 66, 145, 244, 314, 365, 419, 605, 807, 882], "overridden": [16, 28, 139, 815], "regardless": [16, 46, 53, 54, 147, 292, 513, 606], "argument": [16, 28, 55, 56, 59, 66, 141, 161, 162, 163, 175, 182, 183, 184, 186, 187, 188, 189, 220, 222, 266, 272, 279, 280, 281, 333, 339, 344, 385, 391, 397, 441, 447, 454, 455, 456, 486, 491, 494, 495, 511, 516, 522, 527, 562, 565, 570, 587, 591, 597, 606, 711, 712, 792, 813, 841, 864], "caus": [16, 146, 191, 292], "calcul": [16, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 105, 106, 108, 111, 131, 252, 253, 427, 428, 529, 534, 537, 545, 546, 600, 601, 602, 603, 604, 608, 632, 643, 687, 718, 722, 725, 727, 728, 758, 765, 804, 875, 878], "none": [16, 28, 45, 47, 48, 55, 56, 57, 61, 62, 64, 65, 66, 78, 90, 94, 103, 105, 106, 107, 108, 133, 137, 141, 149, 151, 161, 163, 176, 177, 178, 182, 187, 191, 194, 204, 215, 217, 219, 220, 223, 242, 246, 248, 249, 250, 261, 272, 276, 277, 294, 312, 316, 318, 319, 320, 329, 339, 342, 343, 345, 363, 367, 369, 370, 371, 381, 391, 395, 396, 398, 417, 421, 423, 424, 425, 436, 447, 452, 453, 457, 475, 476, 477, 478, 482, 491, 493, 511, 515, 516, 529, 534, 535, 536, 538, 539, 540, 548, 562, 564, 565, 572, 587, 590, 591, 600, 601, 602, 603, 604, 605, 606, 610, 632, 643, 676, 698, 700, 710, 711, 715, 718, 719, 722, 723, 725, 726, 727, 728, 735, 755, 756, 760, 763, 765, 773, 782, 784, 787, 788, 789, 790, 792, 799, 803, 804, 806, 807, 808, 811, 812, 814, 815, 841, 842, 864, 878, 880, 882], "effect": [16, 66, 76, 105, 106, 146, 191, 276, 342, 395, 452, 493, 506, 559, 583, 724, 726, 727, 728], "unless": [16, 28, 53, 72, 145, 842], "substitution_matrix": [16, 60, 61, 62, 63, 64, 65], "suppli": [16, 133, 137, 145, 182, 187, 246, 316, 367, 421, 476, 523, 728, 765], "match_scor": [16, 61, 64, 67], "ad": [16, 60, 61, 62, 63, 64, 65, 137, 147, 215, 457, 529, 534, 714, 717, 841, 880], "occur": [16, 134, 137, 138, 141, 142, 183, 188, 191, 261, 329, 381, 436, 457, 482, 728, 759, 768], "ignor": [16, 47, 69, 78, 105, 106, 134, 135, 136, 137, 138, 141, 142, 146, 149, 248, 249, 292, 293, 318, 319, 369, 370, 423, 424, 477, 509, 561, 586, 600, 601, 602, 603, 604, 719, 726, 727, 765, 784, 819, 841, 842, 878, 880, 882], "mismatch_scor": [16, 61, 64, 67], "subtract": [16, 687], "2d": [16, 60, 61, 62, 63, 64, 65, 103, 107, 108, 111, 495, 510, 519, 537, 606, 715, 722], "dict": [16, 28, 49, 55, 56, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 136, 139, 162, 182, 183, 184, 187, 188, 189, 194, 215, 219, 220, 222, 223, 250, 265, 272, 279, 280, 281, 294, 320, 332, 339, 344, 345, 371, 384, 391, 397, 398, 425, 440, 447, 454, 455, 456, 457, 478, 485, 491, 494, 495, 510, 516, 519, 522, 565, 570, 591, 597, 602, 605, 665, 711, 712, 773, 777, 786, 792, 806, 813, 841, 878, 882], "substitut": [16, 60, 61, 62, 63, 64, 65, 67, 141, 276, 342, 345, 395, 452, 493, 495, 507, 510, 512, 513, 519, 526, 817], "entir": [16, 28, 74, 223, 294, 345, 398, 457], "combin": [16, 28, 45, 48, 139, 534, 601, 700, 714], "enumer": 16, "requir": [16, 78, 84, 85, 94, 105, 106, 131, 134, 135, 137, 140, 144, 147, 148, 219, 279, 292, 293, 454, 545, 547, 572, 602, 608, 698, 718, 726, 757, 763, 797, 817, 841, 876, 878, 882], "suppress_sequ": [16, 66], "zero_index": [16, 66], "wrapper": [16, 66, 84, 85, 818], "otherwis": [16, 29, 45, 48, 57, 72, 73, 137, 139, 142, 145, 146, 191, 276, 342, 395, 452, 493, 496, 497, 499, 504, 509, 549, 550, 552, 557, 561, 573, 574, 576, 581, 586, 589, 605, 793, 878], "inform": [16, 47, 55, 59, 71, 86, 94, 133, 134, 135, 136, 137, 138, 139, 145, 146, 148, 194, 220, 222, 272, 281, 339, 344, 391, 397, 447, 456, 491, 494, 516, 522, 565, 570, 591, 597, 621, 665, 699, 711, 712, 721, 727, 728, 792, 813, 841, 878, 882], "NOT": [16, 88, 191], "meaning": [16, 45, 48, 54, 719, 878], "zhao": [16, 66], "mengyao": [16, 66], "wan": [16, 66], "ping": [16, 66], "lee": [16, 66, 69], "erik": [16, 66], "garrison": [16, 66], "gabor": [16, 66], "marth": [16, 66], "simd": [16, 66], "applic": [16, 47, 60, 66, 760, 882], "plo": [16, 66, 84, 85, 540, 546], "ONE": [16, 66], "2013": [16, 66, 76, 94, 544, 710], "web": [16, 60, 63, 66, 135, 148, 600, 601, 602, 603, 604], "juli": [16, 66], "2014": [16, 66, 133, 144, 534, 544], "http": [16, 47, 60, 61, 62, 63, 64, 65, 66, 69, 73, 83, 108, 131, 132, 133, 134, 135, 136, 137, 138, 139, 142, 144, 145, 146, 147, 148, 282, 290, 291, 517, 540, 544, 546, 548, 566, 572, 584, 592, 600, 601, 602, 603, 604, 710, 814, 815, 840], "www": [16, 60, 63, 66, 83, 108, 131, 133, 134, 135, 136, 137, 138, 139, 144, 148, 282, 290, 291, 601], "ploson": [16, 66], "org": [16, 66, 108, 131, 132, 137, 138, 139, 144, 146, 147, 517, 540, 544, 546, 548, 566, 572, 584, 592, 600, 601, 602, 603, 604, 710, 815], "articl": [16, 66, 135], "info": [16, 66, 204, 223, 294, 345, 398, 457, 609, 665], "doi": [16, 66, 136, 138, 540, 546, 815], "10": [16, 47, 66, 69, 84, 85, 134, 136, 137, 138, 139, 140, 142, 143, 144, 194, 204, 219, 223, 248, 294, 318, 345, 369, 398, 423, 457, 529, 534, 540, 546, 604, 699, 724, 727, 728, 815, 882], "1371": [16, 66, 540, 546], "journal": [16, 66, 69, 72, 79, 94, 95, 97, 99, 139, 540, 546, 600], "pone": [16, 66], "0082138": [16, 66], 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795, 796, 797, 798, 799, 800, 801, 802, 804, 805, 806, 807, 808, 809, 810, 811, 812, 814, 815, 816, 817, 818, 820, 840, 875, 876], "arbitrari": [28, 46, 49, 141, 146, 147, 223, 345, 398, 457, 698, 841, 878], "shallow": [28, 31, 204, 205, 226, 297, 348, 401, 457, 460], "copi": [28, 31, 32, 137, 144, 147, 204, 205, 206, 226, 227, 273, 297, 298, 340, 348, 349, 392, 401, 402, 448, 457, 460, 461, 492, 517, 520, 548, 566, 568, 592, 595, 722, 729, 736, 737, 764, 796, 797, 803, 811, 812, 835, 836, 837], "made": [28, 90, 457, 529, 548, 572, 698, 751, 768, 769, 791, 817], "consum": [28, 48, 163, 223, 282, 345, 398, 457], "abl": [28, 48, 108, 223, 345, 398, 457, 529, 727, 765], "directli": [28, 45, 48, 146, 223, 282, 345, 398, 457, 523, 529, 608, 841, 882], "constructor": [28, 45, 48, 56, 135, 137, 138, 139, 144, 145, 147, 162, 175, 186, 223, 266, 282, 333, 345, 385, 398, 441, 457, 486, 495, 606], "label": [28, 30, 33, 35, 45, 48, 49, 54, 56, 57, 58, 135, 137, 139, 144, 146, 147, 515, 544, 547, 564, 590, 600, 601, 603, 604, 605, 700, 710, 755, 819], "content": [28, 46, 136, 137, 138, 139, 140, 142, 146, 149, 161, 162, 163, 223, 240, 241, 244, 247, 274, 278, 311, 314, 317, 362, 365, 368, 398, 415, 416, 419, 422, 449, 450, 474, 878], "hashabl": [28, 30, 698, 864], "rais": [28, 45, 47, 48, 50, 54, 56, 58, 69, 78, 79, 80, 94, 103, 105, 106, 107, 111, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 137, 138, 144, 149, 150, 161, 162, 163, 182, 183, 184, 185, 187, 188, 189, 218, 225, 241, 242, 246, 248, 250, 261, 262, 264, 265, 267, 268, 269, 270, 276, 292, 294, 296, 311, 312, 316, 318, 320, 329, 331, 332, 334, 335, 336, 337, 342, 347, 362, 363, 367, 369, 371, 381, 383, 384, 386, 387, 388, 389, 395, 400, 416, 417, 421, 423, 425, 436, 437, 439, 440, 442, 443, 444, 445, 452, 459, 474, 475, 476, 478, 482, 484, 485, 487, 488, 489, 490, 493, 499, 506, 507, 509, 510, 511, 514, 521, 524, 525, 531, 538, 539, 545, 552, 559, 561, 562, 563, 569, 576, 583, 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759, 760, 799, 808, 876, 878], "typeerror": [28, 45, 48, 54, 103, 182, 183, 187, 188, 225, 241, 242, 246, 250, 261, 262, 267, 268, 269, 270, 296, 311, 312, 316, 320, 329, 334, 335, 336, 337, 347, 362, 363, 367, 371, 381, 386, 387, 388, 389, 400, 416, 417, 421, 425, 436, 437, 442, 443, 444, 445, 459, 474, 475, 476, 478, 482, 487, 488, 489, 490, 524, 525, 601, 602, 604, 727, 728, 729, 757], "isn": [28, 45, 48, 54, 80, 146, 147, 161, 163, 192, 194, 535, 536, 729], "doe": [28, 45, 46, 48, 54, 57, 66, 78, 94, 133, 135, 137, 138, 140, 142, 144, 147, 191, 241, 282, 283, 289, 292, 311, 362, 416, 474, 507, 517, 524, 547, 566, 589, 592, 600, 602, 604, 643, 719, 727, 728, 751, 760, 771, 784, 797, 804, 807, 814, 818, 876], "exactli": [28, 45, 48, 53, 63, 64, 65, 137, 138, 144, 149, 228, 237, 283, 299, 308, 350, 359, 403, 412, 462, 471, 545, 710, 753], "reassign_index": [28, 45, 48, 57, 58, 144], "neither": [28, 56, 192, 799, 808], "nor": [28, 45, 48, 56, 141, 144, 548, 799], "rangeindex": [28, 45, 48, 56, 144], "stop": [28, 45, 48, 56, 69, 144, 242, 261, 279, 280, 282, 292, 293, 312, 329, 345, 363, 380, 381, 417, 436, 454, 455, 475, 482, 755, 842, 878], "four": [28, 138, 147, 223, 345, 398, 529, 710], "acgt": [28, 45, 48, 49, 51, 52, 58, 224, 228, 237, 241, 252, 253, 258, 260, 262, 266, 295, 299, 308, 311, 326, 328, 333, 346, 350, 359, 362, 377, 379, 385, 399, 403, 412, 416, 427, 428, 433, 435, 437, 441, 457, 458, 462, 471, 474, 480, 481, 486, 495, 513], "ag": [28, 45, 48, 50, 547, 726, 727], "wasn": [28, 138], "non": [28, 72, 80, 133, 135, 136, 140, 146, 194, 223, 259, 271, 275, 294, 327, 338, 341, 345, 378, 390, 394, 398, 434, 446, 451, 495, 526, 527, 528, 529, 531, 534, 538, 539, 541, 542, 543, 572, 600, 603, 604, 608, 713, 719, 724, 759, 760, 765], "seq3": [28, 48, 137, 144], "prob": [28, 33, 46, 53], "iloc": [28, 35], "slice": [28, 35, 230, 248, 249, 263, 273, 301, 318, 319, 330, 340, 352, 369, 370, 382, 392, 405, 423, 424, 438, 448, 464, 477, 483, 492, 499, 547, 552, 576, 740, 878], "axi": [28, 35, 50, 80, 96, 141, 223, 294, 345, 398, 457, 495, 643, 687, 700, 710, 718, 725, 728, 819], "along": [28, 141, 223, 294, 345, 398, 457, 710, 718, 719], "loc": [28, 35, 457, 529, 727], "shape": [28, 40, 49, 131, 143, 495, 497, 527, 528, 530, 531, 532, 533, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 546, 548, 550, 572, 574, 602, 715, 718, 729], "boolean": [29, 106, 137, 140, 145, 194, 223, 230, 243, 245, 248, 251, 263, 266, 268, 270, 271, 273, 301, 313, 315, 318, 321, 330, 333, 335, 337, 338, 340, 345, 352, 364, 366, 369, 372, 382, 385, 387, 389, 390, 392, 393, 398, 405, 418, 420, 423, 426, 438, 441, 443, 445, 446, 448, 457, 464, 483, 486, 488, 490, 492, 587], "OR": 29, "acg": [29, 30, 31, 32, 33, 38, 40, 43, 50, 53, 54, 56, 57, 145, 147, 261, 264, 329, 331, 381, 383, 436, 439, 482, 484], "ac": [29, 30, 31, 32, 33, 38, 40, 43, 46, 48, 50, 54, 56, 57, 60, 63, 136, 138, 139, 147, 194, 251, 321, 372, 426, 878], "No": [29, 73, 133, 134, 136, 145, 148, 204, 239, 310, 361, 414, 473, 602], "search": [30, 60, 133, 134, 137, 219, 248, 261, 318, 329, 369, 381, 423, 436, 482, 496, 549, 573, 714, 763, 768, 769, 770, 771, 838, 878], "l1": 30, "l2": 30, "l3": 30, "__deepcopy__": [31, 205], "msa_copi": [31, 32], "memo": [32, 206, 227, 298, 349, 402, 461], "deep": [32, 70, 206, 226, 227, 297, 298, 348, 349, 401, 402, 457, 460, 461, 508, 520, 560, 568, 585, 595], "__copy__": [32, 206], "deepcopi": [32, 736, 737, 761, 811, 812], "against": [33, 42, 60, 63, 138, 195, 201, 207, 213, 228, 237, 283, 289, 299, 308, 350, 359, 403, 412, 462, 471, 529, 608, 758], "pleas": [35, 55, 59, 137, 145, 220, 222, 272, 281, 339, 344, 391, 397, 447, 456, 491, 494, 516, 522, 565, 570, 591, 597, 711, 712, 792, 813], "restrict": [35, 78, 105, 106, 144, 878], "over": [38, 43, 53, 108, 137, 138, 145, 146, 147, 233, 238, 304, 309, 355, 360, 408, 413, 467, 472, 495, 534, 606, 620, 642, 653, 686, 697, 724, 725, 744, 782, 785, 788, 789, 790, 802, 805, 808, 880], "yield": [38, 43, 53, 137, 219, 233, 238, 247, 248, 249, 263, 264, 280, 293, 304, 309, 317, 318, 319, 330, 331, 355, 360, 368, 369, 370, 382, 383, 408, 413, 422, 423, 424, 438, 439, 455, 467, 472, 477, 483, 484, 604, 770, 782, 785, 788, 789, 790, 799, 805, 807, 808, 842, 876, 882], "size": [40, 76, 495, 534, 548, 572, 600, 601, 602, 604, 687, 698, 710, 718, 724, 726, 727, 728, 840], "1st": [40, 676, 820], "dimens": [40, 143, 144, 495, 505, 527, 531, 535, 536, 548, 558, 572, 582, 604, 700, 709, 710, 719, 720], "equival": [40, 76, 78, 94, 138, 146, 226, 227, 250, 252, 273, 274, 280, 293, 297, 298, 320, 340, 348, 349, 371, 392, 401, 402, 425, 427, 448, 449, 455, 460, 461, 478, 492, 506, 521, 524, 529, 559, 569, 583, 596, 602, 878], "inequ": [42, 201, 213, 237, 289, 308, 359, 412, 471, 572, 719], "__eq__": [42, 213, 504, 557, 581], "revers": [43, 53, 57, 149, 238, 240, 262, 274, 280, 292, 293, 309, 360, 413, 415, 437, 449, 450, 455, 472, 600, 604, 799, 878, 882], "summari": [44, 505, 529, 558, 582], 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"broken": [46, 814], "manner": [46, 137, 144, 230, 244, 301, 314, 352, 365, 405, 419, 464, 602, 719], "present": [46, 47, 78, 105, 106, 133, 137, 143, 146, 147, 205, 206, 223, 240, 243, 244, 245, 250, 251, 261, 271, 274, 292, 313, 314, 315, 320, 321, 329, 338, 345, 364, 365, 366, 371, 372, 381, 390, 393, 398, 415, 418, 419, 420, 425, 426, 436, 446, 449, 478, 482, 509, 529, 561, 586, 600, 601, 603, 604, 643, 709, 719, 728, 729, 759, 814, 815, 817, 880], "default_gap_char": [46, 47, 54, 223, 294, 345, 398], "distinct": [46, 91, 92, 101, 524, 547], "contribut": [46, 94, 608, 713, 718], "AT": [46, 137, 138, 144], "tt": [46, 263, 330, 382, 438, 483], "cg": [46, 273, 340, 392, 448, 457, 492], "degener": [46, 47, 136, 137, 138, 139, 140, 223, 240, 241, 243, 244, 247, 252, 253, 254, 255, 259, 271, 274, 275, 277, 278, 279, 280, 282, 292, 293, 294, 311, 313, 314, 317, 322, 323, 327, 338, 341, 343, 345, 362, 364, 365, 368, 373, 374, 378, 390, 394, 396, 398, 415, 416, 418, 419, 422, 427, 428, 429, 430, 434, 446, 449, 450, 451, 453, 454, 455, 474, 507, 878], "gc": [46, 136, 137, 138, 139, 140, 148, 223, 240, 241, 244, 247, 253, 274, 278, 283, 293, 311, 314, 317, 362, 365, 368, 398, 415, 416, 419, 422, 428, 449, 450, 474, 878], "33": [46, 78, 105, 106, 138, 247, 317, 368, 422, 534, 601, 604, 724, 727, 878], "last": [46, 136, 144, 263, 292, 330, 382, 438, 457, 483, 602, 699, 882], "metric": [47, 69, 74, 78, 79, 94, 103, 104, 105, 106, 107, 108, 109, 110, 111, 138, 246, 316, 367, 421, 476, 511, 525, 562, 572, 587, 735, 875, 878], "inverse_shannon_uncertainti": 47, "degenerate_mod": 47, "gap_mod": 47, "nan": [47, 50, 54, 85, 133, 146, 241, 250, 311, 320, 362, 371, 416, 425, 474, 478, 524, 525, 600, 601, 602, 603, 604, 605, 608, 710, 726, 727, 806, 818], "larger": [47, 727], "mode": [47, 149, 191, 292, 728, 841], "handl": [47, 54, 137, 138, 145, 147, 148, 149, 151, 161, 163, 191, 292, 293, 529, 602, 604, 605, 724, 808, 815, 840, 882], "assign": [47, 56, 67, 103, 107, 144, 146, 195, 273, 340, 392, 448, 457, 492, 513, 529, 534, 600, 603, 604, 698, 728, 754, 755, 756], "np": [47, 50, 78, 85, 94, 105, 106, 133, 223, 225, 242, 243, 245, 246, 250, 251, 261, 262, 267, 268, 269, 270, 271, 276, 296, 312, 313, 315, 316, 320, 321, 329, 334, 335, 336, 337, 338, 342, 345, 347, 363, 364, 366, 367, 371, 372, 381, 386, 387, 388, 389, 390, 393, 395, 398, 400, 417, 418, 420, 421, 425, 426, 436, 437, 442, 443, 444, 445, 446, 452, 457, 459, 475, 476, 478, 482, 487, 488, 489, 490, 493, 495, 524, 525, 527, 528, 530, 531, 532, 533, 534, 535, 536, 537, 538, 540, 541, 542, 543, 544, 546, 547, 600, 602, 603, 604, 605, 608, 609, 698, 699, 710, 723, 724, 726, 727, 728, 729, 777, 799, 814, 818], "remov": [47, 66, 78, 94, 105, 106, 137, 141, 144, 217, 244, 275, 314, 341, 365, 394, 419, 451, 752, 767, 787, 791, 794, 798, 809, 878], "up": [47, 67, 135, 144, 146, 147, 191, 204, 216, 454, 455, 499, 531, 538, 539, 541, 542, 543, 552, 576, 602, 698, 728, 752, 757, 760, 791, 797, 864, 880], "float": 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"alanin": [47, 345], "glycin": [47, 345], "recod": 47, "awar": [47, 94, 146, 457], "consid": [47, 69, 78, 83, 94, 105, 106, 137, 142, 228, 263, 299, 330, 350, 382, 403, 438, 462, 483, 524, 526, 541, 604, 605, 698, 726, 727, 728, 818, 841], "simpli": [47, 54, 101, 149, 282, 517, 566, 592, 719, 724, 768, 882], "minu": [47, 139, 147, 676], "shannon": [47, 82, 95], "uncertainti": [47, 534, 608], "invers": [47, 528, 533, 536, 542], "impli": [47, 191, 608], "higher": [47, 495, 529, 534, 853], "entropi": [47, 82, 97], "make": [47, 54, 137, 142, 146, 149, 283, 499, 524, 552, 576, 600, 604, 728, 803, 806, 807, 815, 821, 841, 882], "symbol": [47, 137], "done": [47, 529, 604, 631, 664, 675], "prefer": [47, 103, 107, 138, 713, 714], "valdar": 47, "residu": [47, 721], "2002": [47, 78, 94, 102, 134, 137], "schneider": 47, "pitfal": 47, "theori": [47, 71, 86, 97, 540, 546], "websit": 47, "ca": [47, 143, 700, 714, 721], "2015": [47, 526, 529, 540, 546], "ncifcrf": 47, "gov": [47, 61, 62, 64, 65, 133, 134, 137, 139, 145, 148, 282, 290, 291], "glossari": 47, "html": [47, 83, 132, 133, 135, 137, 139, 142, 144, 147, 194, 517, 548, 566, 572, 584, 592, 600, 601, 602, 603, 604, 710, 814], "shannon_entropi": 47, "classmethod": [49, 55, 216, 220, 241, 272, 291, 311, 339, 362, 391, 416, 447, 474, 491, 507, 510, 511, 512, 513, 516, 562, 565, 587, 591, 711, 772, 773, 774, 792], "dictionari": [49, 51, 56, 58, 67, 147, 148, 151, 194, 205, 206, 215, 219, 258, 326, 377, 433, 457, 480, 510, 519, 602, 773], "construct": [49, 58, 139, 148, 194, 195, 223, 294, 345, 398, 495, 510, 513, 519, 540, 547, 699, 763, 773, 774, 815, 875, 876, 880], "to_dict": 49, "sort": [49, 54, 109, 110, 195, 204, 207, 247, 250, 276, 317, 320, 342, 368, 371, 395, 422, 425, 452, 478, 493, 643, 676, 698, 801, 806, 807, 814, 878, 882], "rel": [50, 94, 132, 136, 139, 250, 252, 253, 265, 267, 269, 320, 332, 334, 336, 371, 384, 386, 388, 425, 427, 428, 440, 442, 444, 478, 485, 487, 489, 540, 546, 584, 800, 818, 853, 878], "across": [50, 94, 137, 138, 144, 204, 529, 534, 602, 727, 814], "1d": [50, 103, 223, 225, 230, 242, 243, 245, 246, 248, 249, 251, 261, 262, 263, 267, 268, 269, 270, 271, 273, 276, 296, 301, 312, 313, 315, 316, 318, 319, 321, 329, 330, 334, 335, 336, 337, 338, 340, 342, 345, 347, 352, 363, 364, 366, 367, 369, 370, 372, 381, 382, 386, 387, 388, 389, 390, 392, 393, 395, 398, 400, 405, 417, 418, 420, 421, 423, 424, 426, 436, 437, 438, 442, 443, 444, 445, 446, 448, 452, 457, 459, 464, 475, 476, 477, 482, 483, 487, 488, 489, 490, 492, 493], "ndarrai": [50, 107, 223, 225, 242, 243, 245, 246, 251, 261, 262, 267, 268, 269, 270, 271, 276, 296, 312, 313, 315, 316, 321, 329, 334, 335, 336, 337, 338, 342, 345, 347, 363, 364, 366, 367, 372, 381, 386, 387, 388, 389, 390, 393, 395, 398, 400, 417, 418, 420, 421, 426, 436, 437, 442, 443, 444, 445, 446, 452, 457, 459, 475, 476, 482, 487, 488, 489, 490, 493, 499, 517, 527, 528, 530, 531, 532, 533, 535, 536, 537, 538, 539, 541, 542, 543, 544, 548, 552, 566, 576, 584, 589, 592, 606, 608, 722, 729, 772], "vector": [50, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 105, 106, 141, 243, 245, 248, 251, 263, 266, 268, 270, 271, 273, 276, 282, 313, 315, 318, 321, 330, 333, 335, 337, 338, 340, 342, 364, 366, 369, 372, 382, 385, 387, 389, 390, 392, 393, 395, 418, 420, 423, 426, 438, 441, 443, 445, 446, 448, 452, 483, 486, 488, 490, 492, 493, 499, 527, 528, 529, 534, 535, 536, 541, 542, 543, 546, 547, 548, 552, 572, 576, 600, 603, 604, 654, 714, 728, 729, 806, 875], "specifi": [50, 54, 94, 111, 133, 135, 137, 138, 139, 140, 141, 144, 147, 148, 149, 181, 191, 194, 204, 217, 219, 223, 230, 248, 250, 266, 279, 291, 292, 294, 301, 318, 320, 333, 345, 352, 369, 371, 385, 398, 405, 423, 425, 441, 454, 457, 464, 478, 486, 496, 499, 506, 509, 514, 515, 521, 527, 528, 529, 534, 535, 536, 538, 539, 545, 549, 552, 559, 561, 563, 564, 569, 573, 576, 583, 586, 588, 590, 596, 600, 601, 602, 603, 604, 608, 687, 710, 718, 719, 725, 757, 765, 796, 799, 801, 804, 807, 814, 841, 853, 854, 864, 875, 882], "Will": [50, 181, 184, 189, 191, 508, 520, 560, 568, 585, 595, 700, 729], "least": [51, 52, 90, 142, 146, 248, 257, 258, 260, 318, 325, 326, 328, 369, 376, 377, 379, 423, 432, 433, 435, 479, 480, 481, 529, 602, 710, 727, 728, 817, 882], "demonstr": [51, 52, 149, 258, 260, 326, 328, 377, 379, 433, 435, 480, 481], "behavior": [51, 52, 54, 60, 61, 62, 137, 138, 139, 146, 191, 258, 260, 276, 292, 326, 328, 342, 377, 379, 395, 433, 435, 452, 457, 480, 481, 493, 600, 602, 604, 759, 882], "rang": [52, 74, 83, 95, 106, 138, 139, 146, 240, 244, 250, 260, 263, 274, 314, 320, 328, 330, 365, 371, 379, 382, 415, 419, 425, 435, 438, 449, 478, 481, 483, 600, 601, 710, 728, 777, 882], "qualiti": [52, 137, 145, 223, 228, 240, 244, 260, 274, 299, 314, 328, 345, 350, 365, 379, 398, 403, 415, 419, 435, 449, 457, 462, 481, 710, 878], "ignore_metadata": 53, "improv": [53, 142, 144, 223, 345, 398, 587], "__iter__": 53, "__reversed__": 53, "concat": [53, 54], "artifact": [53, 60, 61, 62], "real": [53, 137, 138, 145, 526, 527, 528, 532, 533, 535, 536, 541, 542, 543], "concaten": [53, 147, 216, 241, 311, 362, 416, 474], "outer": [53, 54, 241, 311, 362, 416, 474, 510], "join": [53, 133, 134, 138, 145, 147, 148, 241, 311, 362, 416, 474, 807, 814, 815], "aa": [53, 137, 139, 144, 282], "gt": 53, "strict": [54, 144, 241, 311, 362, 416, 474, 509, 561, 586, 602, 605, 608], "horizont": 54, "control": [54, 137, 600, 602, 603, 609, 721, 724, 726, 727, 728], "dure": [54, 137, 195, 241, 311, 362, 416, 474, 604, 839], "section": [54, 137, 138, 143, 146, 147, 282, 457, 601, 602, 713, 714], "inner": [54, 142, 241, 311, 362, 416, 474, 510], "left": [54, 69, 97, 142, 527, 528, 532, 537, 541, 542, 543, 544, 755, 777, 818, 819, 880], "right": [54, 69, 97, 142, 526, 527, 528, 532, 537, 541, 542, 543, 544, 777, 818, 819, 882], "unshar": 54, "pad": [54, 144, 241, 311, 362, 416, 474], "guarante": [54, 85, 146, 223, 247, 317, 345, 368, 398, 422, 548, 606, 765], "duplic": [54, 111, 138, 146, 147, 218, 276, 342, 395, 452, 493, 509, 561, 586, 730, 838], "doesn": [54, 137, 146, 185, 292, 541, 545, 599, 713, 719, 723, 797, 816, 881], "subclass": [54, 135, 137, 144, 147, 149, 241, 311, 362, 416, 457, 474, 495, 547, 548, 606, 814, 841], "togeth": [54, 136, 137, 139, 147, 529, 841], "likewis": [54, 94, 147], "per": [54, 133, 134, 145, 147, 223, 345, 398, 457, 534, 605, 608, 698, 721, 727, 728, 753, 840], "retain": [54, 241, 273, 311, 340, 362, 392, 416, 448, 474, 492, 509, 561, 586, 698], "output": [54, 133, 134, 142, 144, 145, 147, 266, 333, 385, 441, 486, 534, 600, 604, 605, 643, 714, 807, 815, 882], "reproduc": [54, 78, 105, 106], "necessari": [54, 133, 144, 204, 457, 548, 600, 601, 602, 631, 664, 675, 760, 839, 876], "msa1": 54, "msa2": 54, "unnecessari": 54, "By": [54, 83, 94, 103, 107, 137, 139, 146, 529, 604, 718, 719, 722, 804, 815, 842], "col1": [54, 146], "43": [54, 90, 143, 814], "col2": [54, 146], "col3": [54, 146], "o": [54, 55, 59, 94, 136, 137, 138, 145, 147, 220, 222, 272, 281, 339, 344, 345, 391, 397, 447, 456, 491, 494, 516, 522, 565, 570, 591, 597, 711, 712, 792, 813, 815, 875, 881], "file": [55, 59, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 162, 175, 182, 183, 184, 186, 187, 188, 189, 190, 191, 192, 193, 220, 222, 272, 281, 339, 344, 391, 397, 447, 456, 491, 494, 515, 516, 522, 529, 547, 564, 565, 570, 590, 591, 597, 631, 664, 675, 710, 711, 712, 726, 755, 792, 813, 839, 840, 875, 880], "kwarg": [55, 59, 66, 103, 107, 108, 111, 112, 161, 163, 175, 182, 183, 184, 186, 187, 188, 189, 192, 193, 220, 222, 272, 279, 280, 281, 339, 344, 391, 397, 447, 454, 455, 456, 491, 494, 495, 516, 522, 565, 570, 591, 597, 687, 711, 712, 792, 813, 841, 876], "instanc": [55, 59, 149, 163, 176, 178, 179, 180, 182, 187, 204, 219, 220, 222, 241, 272, 281, 311, 339, 344, 362, 391, 397, 416, 447, 456, 474, 491, 494, 497, 507, 516, 522, 524, 525, 534, 548, 550, 565, 570, 572, 574, 589, 591, 597, 602, 604, 605, 606, 620, 642, 653, 686, 697, 710, 711, 712, 728, 735, 751, 792, 813, 814, 821, 822, 825, 832, 880, 882], "registri": [55, 59, 132, 137, 138, 145, 220, 222, 272, 281, 339, 344, 391, 397, 447, 456, 491, 494, 516, 522, 565, 570, 591, 597, 711, 712, 792, 813, 876], "system": [55, 59, 86, 97, 146, 148, 149, 204, 220, 222, 272, 281, 339, 344, 391, 397, 447, 456, 491, 494, 516, 522, 565, 570, 591, 597, 711, 712, 727, 792, 813], "clustal": [55, 59, 114, 876], "fasta": [55, 59, 116, 138, 140, 145, 272, 281, 339, 344, 391, 397, 447, 456, 491, 494, 876], "fastq": [55, 59, 117, 145, 272, 281, 339, 344, 391, 397, 447, 456, 491, 494, 876], "phylip": [55, 59, 126, 137, 142, 814, 876, 880], "stockholm": [55, 59, 129], "filepath": [55, 59, 182, 183, 184, 187, 188, 189, 191, 220, 222, 272, 281, 339, 344, 391, 397, 447, 456, 491, 494, 516, 522, 565, 570, 591, 597, 605, 711, 712, 792, 813], "url": [55, 59, 182, 183, 184, 187, 188, 189, 191, 220, 222, 272, 281, 339, 344, 391, 397, 447, 456, 491, 494, 516, 522, 565, 570, 591, 597, 711, 712, 792, 813], "filehandl": [55, 59, 149, 161, 162, 163, 182, 183, 184, 187, 188, 189, 191, 192, 220, 222, 272, 281, 339, 344, 391, 397, 447, 456, 491, 494, 516, 522, 565, 570, 591, 597, 711, 712, 792, 813], "etc": [55, 59, 80, 137, 138, 146, 182, 183, 184, 187, 188, 189, 194, 220, 222, 272, 281, 339, 344, 391, 397, 447, 456, 491, 494, 495, 516, 522, 565, 570, 591, 597, 711, 712, 719, 721, 735, 792, 813, 878], "someth": [55, 59, 149, 162, 182, 183, 184, 187, 188, 189, 220, 222, 272, 281, 339, 344, 391, 397, 447, 456, 491, 494, 516, 522, 565, 570, 591, 597, 606, 711, 712, 792, 813, 882], "understood": [55, 59, 142, 182, 183, 184, 187, 188, 189, 220, 222, 272, 281, 339, 344, 391, 397, 447, 456, 491, 494, 516, 522, 565, 570, 591, 597, 711, 712, 792, 813], "util": [55, 59, 148, 161, 163, 220, 222, 272, 281, 282, 290, 291, 294, 339, 344, 391, 397, 447, 456, 491, 494, 516, 522, 565, 570, 591, 597, 711, 712, 792, 813, 875, 876], "close": [55, 59, 79, 137, 138, 142, 144, 147, 191, 192, 220, 222, 272, 281, 292, 339, 344, 391, 397, 447, 456, 491, 494, 516, 522, 529, 565, 570, 591, 597, 631, 664, 675, 711, 712, 792, 813, 840], "respons": [55, 59, 220, 222, 272, 281, 339, 344, 391, 397, 447, 456, 491, 494, 516, 522, 565, 570, 591, 597, 631, 664, 675, 699, 711, 712, 714, 721, 792, 813], "caller": [55, 59, 220, 222, 272, 281, 339, 344, 391, 397, 447, 456, 491, 494, 516, 522, 565, 570, 591, 597, 631, 664, 675, 711, 712, 792, 813], "reader": [55, 131, 132, 133, 134, 135, 136, 138, 141, 142, 143, 144, 145, 146, 147, 148, 149, 151, 162, 176, 181, 182, 183, 187, 188, 220, 272, 339, 391, 447, 491, 516, 565, 591, 711, 792], "attempt": [55, 137, 146, 191, 220, 272, 339, 391, 447, 491, 516, 565, 591, 711, 755, 768, 792], "guess": [55, 90, 112, 137, 182, 187, 220, 272, 339, 391, 447, 491, 516, 565, 591, 711, 792, 817], "keyword": [55, 59, 66, 136, 139, 141, 162, 182, 183, 184, 187, 188, 189, 219, 220, 222, 266, 272, 279, 280, 281, 333, 339, 344, 385, 391, 397, 441, 447, 454, 455, 456, 486, 491, 494, 516, 522, 565, 570, 591, 597, 711, 712, 792, 813], "write": [55, 132, 135, 136, 138, 140, 141, 142, 144, 147, 149, 163, 180, 181, 191, 220, 272, 339, 391, 447, 491, 516, 547, 565, 591, 631, 664, 675, 711, 749, 792, 820], "reassign": [56, 144, 602], "remain": [56, 137], "ccg": 56, "altern": [56, 148, 149, 275, 292, 341, 394, 451, 511, 526, 540, 546, 562, 587, 602, 604, 605, 608, 719, 724, 773, 799], "ascend": [57, 221], "place": [57, 142, 147, 292, 698, 719, 722, 752, 777, 809, 819], "multiindex": [57, 594], "noth": [57, 191, 277, 343, 396, 453, 841], "descend": [57, 94, 221, 735, 765, 777, 785, 794, 801, 802, 805, 808, 880], "sort_index": 57, "passthrough": 57, "intern": [57, 132, 139, 142, 545, 753, 755, 757, 763, 765, 768, 777, 786, 791, 797, 807, 809, 810, 876, 880], "identifi": [57, 103, 107, 108, 111, 131, 135, 137, 138, 139, 140, 141, 144, 147, 148, 219, 248, 369, 423, 547, 605, 724, 728, 876], "modifi": [57, 137, 139, 147, 181, 223, 345, 398, 457, 589, 687, 720, 799], "from_dict": [58, 600, 604, 609, 710, 726, 727], "regist": [59, 149, 150, 151, 161, 162, 163, 175, 181, 183, 186, 188, 222, 281, 344, 397, 456, 494, 522, 570, 597, 712, 813], "writer": [59, 131, 132, 133, 134, 135, 136, 138, 139, 141, 142, 143, 144, 145, 146, 147, 148, 149, 151, 178, 181, 184, 189, 191, 222, 281, 344, 397, 456, 494, 522, 570, 597, 712, 813], "penalize_terminal_gap": [60, 61, 62], "unalign": [60, 61, 62, 63, 64, 65, 66, 878], "substract": [60, 61, 62, 63, 64, 65, 717], "typic": [60, 61, 62, 63, 64, 65, 67, 137, 138, 145, 146, 147, 194, 204, 719, 755], "similar": [60, 61, 62, 63, 64, 65, 104, 134, 136, 137, 138, 141, 144, 146, 149, 457, 495, 600, 601, 602, 603, 604, 714, 719, 721, 727, 728, 878, 880], "lookup": [60, 61, 62, 63, 64, 65, 176, 177, 178, 499, 552, 576, 599, 602, 605, 752, 763, 767, 777, 778, 787, 791, 806, 841], "continu": [60, 61, 62, 699], "penal": [60, 61, 62], "even": [60, 61, 62, 68, 82, 88, 95, 99, 137, 142, 292, 600, 604, 728, 808], "irrelev": [60, 61, 62], "want": [60, 61, 62, 136, 139, 204, 724, 726, 727, 728, 759, 760, 876], "nearli": [60, 61, 62], "tupl": [60, 61, 62, 63, 64, 65, 66, 73, 77, 84, 90, 93, 111, 140, 162, 194, 215, 219, 279, 280, 454, 455, 495, 499, 548, 552, 572, 576, 774, 775, 806, 807], "input": [60, 61, 62, 63, 64, 65, 66, 78, 94, 103, 105, 106, 107, 148, 161, 163, 191, 192, 204, 216, 246, 273, 292, 293, 316, 340, 367, 392, 421, 448, 476, 492, 523, 529, 534, 545, 548, 601, 602, 698, 710, 713, 714, 716, 720, 729, 809, 814, 815, 875, 876, 878], "item": [60, 61, 62, 63, 64, 65, 66, 147, 250, 273, 320, 340, 371, 392, 425, 448, 457, 478, 492, 506, 521, 559, 569, 583, 596, 698, 729, 757, 799, 806, 807, 841, 842, 852, 882], "local_pairwise_align": [60, 61, 62, 64, 65], 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\ No newline at end of file