From b42eebc01bc5d06ec6a2c6e2f85f8b778f063512 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Camilo=20Garc=C3=ADa?= <cgarci39@eafit.edu.co>
Date: Thu, 8 Sep 2022 19:22:08 -0500
Subject: [PATCH] update version news and history

---
 HISTORY.qmd                                   |  15 +
 NEWS.md                                       |   7 +-
 docs/HISTORY.html                             |  40 +-
 .../intro-structural-bioinfo.html             |  80 ++-
 .../chs-bio-structural/molecular-docking.html |  50 +-
 .../seq-analysis-challenges.html              |  40 +-
 .../chs-challenges-demos/unix-challenges.html |  42 +-
 docs/chs-command-line/git-and-github.html     |  50 +-
 docs/chs-command-line/hpc-notions.html        |  40 +-
 docs/chs-command-line/package-managers.html   |  40 +-
 .../welcome-to-command-line.html              |  56 +-
 docs/chs-genomics/comparative-genomics.html   | 610 ++++++++++++++++++
 docs/chs-genomics/functional-genomics.html    |  46 +-
 docs/chs-genomics/genome-annotation.html      |  40 +-
 docs/chs-genomics/genome-assembly.html        |  42 +-
 .../variant-calling-analysis.html             |  40 +-
 .../phylogenetic-reconstructions.html         |  42 +-
 docs/chs-phylogenetics/phylogenomics.html     |  65 +-
 .../NGS-TGS-principles.html                   |  40 +-
 .../introduction-to-sequence-analysis.html    |  42 +-
 .../sanger-analysis.html                      |  50 +-
 .../sequence-alignments.html                  |  40 +-
 docs/index.html                               |  40 +-
 docs/intro.html                               |  40 +-
 docs/references.html                          |  40 +-
 docs/search.json                              |  27 +-
 docs/sitemap.xml                              |  56 +-
 27 files changed, 1409 insertions(+), 311 deletions(-)
 create mode 100644 docs/chs-genomics/comparative-genomics.html

diff --git a/HISTORY.qmd b/HISTORY.qmd
index 9fd69e7..bd5f348 100644
--- a/HISTORY.qmd
+++ b/HISTORY.qmd
@@ -1,5 +1,20 @@
 # History {.unnumbered}
 
+## Edition 0.0.9
+
+- Starting the Sanger chapter
+
+- More on Seq. analysis
+
+- Keep history on book and add dates
+
+- Change the cover
+
+- Add new parts and chapters outlines (phylogenetics and metagenomics)
+
+- New challenges on seq analysis solved
+
+
 ## Ed. 0.0.8 (2022-08-29)
 
 - New render w/ Quarto 1.1
diff --git a/NEWS.md b/NEWS.md
index f223d06..03c23f7 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -6,4 +6,9 @@
 
 - Keep history on book and add dates
 
-- Move citations per chapter (TODO)
+
+- Change the cover
+
+- Add new parts and chapters outlines (phylogenetics and metagenomics)
+
+- New challenges on seq analysis solved
\ No newline at end of file
diff --git a/docs/HISTORY.html b/docs/HISTORY.html
index c4dc7d7..278002a 100644
--- a/docs/HISTORY.html
+++ b/docs/HISTORY.html
@@ -207,7 +207,7 @@ <h1 class="quarto-secondary-nav-title">History</h1>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="./chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
   </div>
 </li>
       </ul>
@@ -239,12 +239,17 @@ <h1 class="quarto-secondary-nav-title">History</h1>
   <div class="sidebar-item-container"> 
   <a href="./chs-genomics/functional-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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@@ -252,24 +257,39 @@ <h1 class="quarto-secondary-nav-title">History</h1>
       <ul id="quarto-sidebar-section-5" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="./chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="./chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
   </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
@@ -284,12 +304,12 @@ <h1 class="quarto-secondary-nav-title">History</h1>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./HISTORY.html" class="sidebar-item-text sidebar-link active">History</a>
diff --git a/docs/chs-bio-structural/intro-structural-bioinfo.html b/docs/chs-bio-structural/intro-structural-bioinfo.html
index 934318f..1a2cfaa 100644
--- a/docs/chs-bio-structural/intro-structural-bioinfo.html
+++ b/docs/chs-bio-structural/intro-structural-bioinfo.html
@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>Fundamentals of computational biology - 15&nbsp; Structural bioinformatics</title>
+<title>Fundamentals of computational biology - 17&nbsp; Structural bioinformatics</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -31,7 +31,7 @@
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
 <link href="../chs-bio-structural/molecular-docking.html" rel="next">
-<link href="../chs-genomics/functional-genomics.html" rel="prev">
+<link href="../chs-metagenomics/metagenomic-sequencing.html" rel="prev">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
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@@ -77,7 +77,7 @@
 
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-<meta name="citation_title" content="[[15]{.chapter-number}&nbsp; [Structural bioinformatics]{.chapter-title}]{#sec-biostructural .quarto-section-identifier}">
+<meta name="citation_title" content="[[17]{.chapter-number}&nbsp; [Structural bioinformatics]{.chapter-title}]{#sec-biostructural .quarto-section-identifier}">
 <meta name="citation_fulltext_html_url" content="https://camilogarciabotero.github.io/biocomp-book//chs-bio-structural/intro-structural-bioinfo.html">
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     <div class="container-fluid d-flex justify-content-between">
-      <h1 class="quarto-secondary-nav-title"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></h1>
+      <h1 class="quarto-secondary-nav-title"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></h1>
       <button type="button" class="quarto-btn-toggle btn" aria-label="Show secondary navigation">
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@@ -209,7 +209,7 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">15</span>&nb
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
   </div>
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@@ -241,12 +241,17 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">15</span>&nb
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   <a href="../chs-genomics/functional-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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@@ -254,24 +259,39 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">15</span>&nb
       <ul id="quarto-sidebar-section-5" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link active"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link active"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
   </div>
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       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
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-      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
@@ -286,12 +306,12 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">15</span>&nb
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
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-      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">  
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   <div class="sidebar-item-container"> 
   <a href="../HISTORY.html" class="sidebar-item-text sidebar-link">History</a>
@@ -313,12 +333,12 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">15</span>&nb
     <h2 id="toc-title">Table of contents</h2>
    
   <ul>
-  <li><a href="#protein-structures" id="toc-protein-structures" class="nav-link active" data-scroll-target="#protein-structures"><span class="toc-section-number">15.1</span>  Protein structures</a></li>
-  <li><a href="#identifying-or-predicting-protein-structures" id="toc-identifying-or-predicting-protein-structures" class="nav-link" data-scroll-target="#identifying-or-predicting-protein-structures"><span class="toc-section-number">15.2</span>  Identifying or predicting protein structures</a>
+  <li><a href="#protein-structures" id="toc-protein-structures" class="nav-link active" data-scroll-target="#protein-structures"><span class="toc-section-number">17.1</span>  Protein structures</a></li>
+  <li><a href="#identifying-or-predicting-protein-structures" id="toc-identifying-or-predicting-protein-structures" class="nav-link" data-scroll-target="#identifying-or-predicting-protein-structures"><span class="toc-section-number">17.2</span>  Identifying or predicting protein structures</a>
   <ul class="collapse">
-  <li><a href="#secondary-structure-prediction" id="toc-secondary-structure-prediction" class="nav-link" data-scroll-target="#secondary-structure-prediction"><span class="toc-section-number">15.2.1</span>  Secondary structure prediction</a></li>
+  <li><a href="#secondary-structure-prediction" id="toc-secondary-structure-prediction" class="nav-link" data-scroll-target="#secondary-structure-prediction"><span class="toc-section-number">17.2.1</span>  Secondary structure prediction</a></li>
   </ul></li>
-  <li><a href="#pdb-database-introduction" id="toc-pdb-database-introduction" class="nav-link" data-scroll-target="#pdb-database-introduction"><span class="toc-section-number">15.3</span>  PDB database introduction</a></li>
+  <li><a href="#pdb-database-introduction" id="toc-pdb-database-introduction" class="nav-link" data-scroll-target="#pdb-database-introduction"><span class="toc-section-number">17.3</span>  PDB database introduction</a></li>
   </ul>
 <div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/camilogarciabotero/biocomp-book/edit/main/chs-bio-structural/intro-structural-bioinfo.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/camilogarciabotero/biocomp-book/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
     </div>
@@ -327,7 +347,7 @@ <h2 id="toc-title">Table of contents</h2>
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
-<h1 class="title"><span id="sec-biostructural" class="quarto-section-identifier d-none d-lg-block"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></span></h1>
+<h1 class="title"><span id="sec-biostructural" class="quarto-section-identifier d-none d-lg-block"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></span></h1>
 </div>
 
 
@@ -344,15 +364,15 @@ <h1 class="title"><span id="sec-biostructural" class="quarto-section-identifier
 <p>Structural bioinformatics is a multidisciplinary area enriched by chemistry, physics, computer science and many others. Although, it could be focused on different biological macro-molecules, here the emphasis will be focused on proteins.</p>
 <p>One of the first protein structure elucidated was myoglobin and it triggered the study of the role of the structure of proteins and its biological functions</p>
 <p>Identify a protein related to your study that could be further analyzed.</p>
-<section id="protein-structures" class="level2" data-number="15.1">
-<h2 data-number="15.1" class="anchored" data-anchor-id="protein-structures"><span class="header-section-number">15.1</span> Protein structures</h2>
+<section id="protein-structures" class="level2" data-number="17.1">
+<h2 data-number="17.1" class="anchored" data-anchor-id="protein-structures"><span class="header-section-number">17.1</span> Protein structures</h2>
 <p>Difference between the levels of protein structure primary structure is the basic linear representation of aminoacids. Natural aminoacids and modified or rare aminoacids display physico-chemical rich information and could be represented by letters. Therefore in the genetic code we could find the one-letter code.</p>
 <p>Secondary structures result from the spatial arrangement of aminoacids that interact with each closer neighbors. There are some remarkable secondary structures such as <span class="math inline">\(\beta\)</span>-sheets, <span class="math inline">\(\alpha\)</span>-helix, coils (flexible) and others.</p>
 <p>Tertiary structure informs about the structural disposition of the secondary structures that fold between each other due to hydrophobic interactions, disulfure bonds, and other chemical interactions forming a globular and dynamic structure. Thus, proteins could display multiple structural states depending on the physical and energy stability (see the <a href="https://en.wikipedia.org/wiki/Levinthal%27s_paradox">:Levinthal’s paradox</a>).</p>
 <p>Quaternary structures result from interaction of multiple tertiary structures. <em>The structure, therefore dictates the protein function</em>. This basic concept have triggered more recently a boom on the analysis of the structure of proteins.</p>
 </section>
-<section id="identifying-or-predicting-protein-structures" class="level2 page-columns page-full" data-number="15.2">
-<h2 data-number="15.2" class="anchored" data-anchor-id="identifying-or-predicting-protein-structures"><span class="header-section-number">15.2</span> Identifying or predicting protein structures</h2>
+<section id="identifying-or-predicting-protein-structures" class="level2 page-columns page-full" data-number="17.2">
+<h2 data-number="17.2" class="anchored" data-anchor-id="identifying-or-predicting-protein-structures"><span class="header-section-number">17.2</span> Identifying or predicting protein structures</h2>
 <p>Xray crystallography, nuclear magnetic resonance (NMR) allows to encapsulated dynamic information of the protein in time Electron micrography (EM) and Cryo-EM. These experiment rely on highly specialized set ups and there are other drawbacks.</p>
 <div class="page-columns page-full"><p></p><div class="no-row-height column-margin column-container"><span class="aside">To date, helium is scarce around the world, so labs all around are having trouble to get this element.</span></div></div>
 <p>Modelling the structure whether <em>ab initio</em> or by <em>homology</em> also allow structure prediction. However these strategies</p>
@@ -361,8 +381,8 @@ <h2 data-number="15.2" class="anchored" data-anchor-id="identifying-or-predictin
 <p>Protein topologies resulting from the folding: horshoe, beta-barrel and other could be identified</p>
 <p>Structural classification of proteins (SCOP) when analyzing a new protein classification by class, architecture, topology (fold-family), homologous superfamily and sequence family</p>
 <p>Importance of Gene Ontology</p>
-<section id="secondary-structure-prediction" class="level3 page-columns page-full" data-number="15.2.1">
-<h3 data-number="15.2.1" class="anchored" data-anchor-id="secondary-structure-prediction"><span class="header-section-number">15.2.1</span> Secondary structure prediction</h3>
+<section id="secondary-structure-prediction" class="level3 page-columns page-full" data-number="17.2.1">
+<h3 data-number="17.2.1" class="anchored" data-anchor-id="secondary-structure-prediction"><span class="header-section-number">17.2.1</span> Secondary structure prediction</h3>
 <p>Secondary structures could also be represented in one letter (e.g.)</p>
 <p>Functional domains could be predicted by sequence alignment and allow structural inference. Main predictions are based heavily on machine learning and are frequently accepted under a consensus of multiple tools.</p>
 <div class="page-columns page-full"><p></p><div class="no-row-height column-margin column-container"><span class="aside">There is a group of protein called intrinsically-disordered proteins that change in its tertiary structures quite frequently, therefore it prediction could be troublesome.</span></div></div>
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 </div>
 </section>
 </section>
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-<h2 data-number="15.3" class="anchored" data-anchor-id="pdb-database-introduction"><span class="header-section-number">15.3</span> PDB database introduction</h2>
+<section id="pdb-database-introduction" class="level2" data-number="17.3">
+<h2 data-number="17.3" class="anchored" data-anchor-id="pdb-database-introduction"><span class="header-section-number">17.3</span> PDB database introduction</h2>
 <p>The PDB database is one of the most important and ancient open biological database where all new protein structures are submitted. It is an international consortium where several regions work together to curate information.</p>
 <p>The PDB in Europe (<a href="pdbe.org">PDBe</a>) is not only for proteins but form many other <em>experimentally predicted</em> macro-molecules (protein-protein interactions, peptides, RNA and so on).</p>
 <p>Protein structures are registered using a unique code of four characters.</p>
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-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></span>
+      <a href="../chs-metagenomics/metagenomic-sequencing.html" class="pagination-link">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></span>
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+        <span class="nav-page-text"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></span> <i class="bi bi-arrow-right-short"></i>
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-      <h1 class="quarto-secondary-nav-title"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></h1>
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-  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
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+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
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+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
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+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
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-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link active"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link active"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
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+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
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       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
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             <i class="bi bi-chevron-right ms-2"></i>
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+<h1 class="title"><span id="sec-molecular-docking" class="quarto-section-identifier d-none d-lg-block"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></span></h1>
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-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></span>
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></span>
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diff --git a/docs/chs-challenges-demos/seq-analysis-challenges.html b/docs/chs-challenges-demos/seq-analysis-challenges.html
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-  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
   </div>
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   <a href="../chs-genomics/functional-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
       </ul>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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 <li class="sidebar-item">
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-  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+</li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
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+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">
+<li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
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 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
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       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
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 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
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-      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">
+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../HISTORY.html" class="sidebar-item-text sidebar-link">History</a>
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-  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
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   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
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 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+</li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">
+<li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
   </div>
 </li>
       </ul>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link active">Unix challenges</a>
@@ -330,12 +350,12 @@ <h1 class="quarto-secondary-nav-title">Unix challenges</h1>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">
+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../HISTORY.html" class="sidebar-item-text sidebar-link">History</a>
@@ -717,7 +737,7 @@ <h1 class="title d-none d-lg-block">Unix challenges</h1>
 </script><script src="https://giscus.app/client.js" data-repo="camilogarciabotero/biocomp-book" data-repo-id="R_kgDOHKOnSw" data-category="General" data-category-id="DIC_kwDOHKOnS84CQ7NN" data-mapping="title" data-reactions-enabled="1" data-emit-metadata="0" data-input-position="top" data-theme="light" data-lang="en" crossorigin="anonymous" async="">
 </script><nav class="page-navigation"><div class="nav-page nav-page-previous">
       <a href="../chs-bio-structural/molecular-docking.html" class="pagination-link">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></span>
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
diff --git a/docs/chs-command-line/git-and-github.html b/docs/chs-command-line/git-and-github.html
index b07e597..36c932d 100644
--- a/docs/chs-command-line/git-and-github.html
+++ b/docs/chs-command-line/git-and-github.html
@@ -256,7 +256,7 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">2</span>&nbs
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
   </div>
 </li>
       </ul>
@@ -288,12 +288,17 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">2</span>&nbs
   <div class="sidebar-item-container"> 
   <a href="../chs-genomics/functional-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
       </ul>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
@@ -301,24 +306,39 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">2</span>&nbs
       <ul id="quarto-sidebar-section-5" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+</li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">
+<li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
   </div>
 </li>
       </ul>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
@@ -333,12 +353,12 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">2</span>&nbs
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">
+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../HISTORY.html" class="sidebar-item-text sidebar-link">History</a>
@@ -410,7 +430,7 @@ <h1 class="title"><span id="sec-vcs" class="quarto-section-identifier d-none d-l
 </section><section id="the-local-workflow" class="level3" data-number="2.2.2"><h3 data-number="2.2.2" class="anchored" data-anchor-id="the-local-workflow">
 <span class="header-section-number">2.2.2</span> The local workflow</h3>
 <div class="quarto-figure quarto-figure-center">
-<figure class="figure"><p><a href="imgs-cli/gitlocal.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" title="Local workflow of a git project adding and committing changes"><img src="imgs-cli/gitlocal.png" class="img-fluid figure-img" style="width:60.0%"></a></p>
+<figure class="figure"><p><a href="imgs-cli/gitlocal.png" class="lightbox" title="Local workflow of a git project adding and committing changes" data-gallery="quarto-lightbox-gallery-1"><img src="imgs-cli/gitlocal.png" class="img-fluid figure-img" style="width:60.0%"></a></p>
 <p></p><figcaption class="figure-caption">Local workflow of a git project adding and committing changes</figcaption><p></p>
 </figure>
 </div>
@@ -420,7 +440,7 @@ <h1 class="title"><span id="sec-vcs" class="quarto-section-identifier d-none d-l
 <p>As mention before, one of the great advantages that git can later achieve is to collaborate. However, to get into that a sharable server must allow users to have a common ground, and this is what <a href="https://github.com/home">GitHub</a> allow. GitHub is a web platform where the local repositories become public and any user can access to the controlled versions of an image of your repo. The famous pet is the octocat <a href="#fig-octocat">Fig.&nbsp;<span>2.1</span></a></p>
 
 <div class="no-row-height column-margin column-container"><div id="fig-octocat" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-cli/octocat.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2" title="The octocat from GitHub"><img src="imgs-cli/octocat.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-cli/octocat.png" class="lightbox" title="The octocat from GitHub" data-gallery="quarto-lightbox-gallery-2"><img src="imgs-cli/octocat.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;2.1: The octocat from GitHub</figcaption><p></p>
 </figure>
 </div></div><p>To enable the communication with a remote repo, git has encoded many specific commands, once the repos are <strong>cloned</strong> a simple workflow from the own local and remote repos is made possible thanks to two simple commands <code>git push</code> and <code>git pull</code>.</p>
@@ -443,7 +463,7 @@ <h1 class="title"><span id="sec-vcs" class="quarto-section-identifier d-none d-l
 </div>
 </div>
 <div id="fig-cloning" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-cli/gitcloning.png" class="lightbox" data-gallery="quarto-lightbox-gallery-3" title="The cloning workflow in brief"><img src="imgs-cli/gitcloning.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-cli/gitcloning.png" class="lightbox" title="The cloning workflow in brief" data-gallery="quarto-lightbox-gallery-3"><img src="imgs-cli/gitcloning.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;2.2: The cloning workflow in brief</figcaption><p></p>
 </figure>
 </div>
@@ -465,7 +485,7 @@ <h1 class="title"><span id="sec-vcs" class="quarto-section-identifier d-none d-l
 <span class="header-section-number">2.3.1</span> Forking and collaborate</h3>
 <p>Basic collaboration on an open repository is a three-step process. First you need to <code>fork</code> the repo, this will create a mirror copy of the repo in your GitHub profile. In a second step, a simple <code>clone</code> of the repo will generate a copy of the forked repo on your local machine, so you can freely work and make your mistakes and push them to your forked repo that belongs to your account. In a third step, once they are on the remote repo you will have to create a <code>pull request</code> (PR), as its name suggest: you are <strong>asking</strong> the owners of the original to consider your changes <a href="#fig-forking">Fig.&nbsp;<span>2.3</span></a>.</p>
 <div id="fig-forking" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-cli/gitforking.png" class="lightbox" data-gallery="quarto-lightbox-gallery-4" title="A common collaborative workflow from GitHub, using fork, clone and pull requests"><img src="imgs-cli/gitforking.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-cli/gitforking.png" class="lightbox" title="A common collaborative workflow from GitHub, using fork, clone and pull requests" data-gallery="quarto-lightbox-gallery-4"><img src="imgs-cli/gitforking.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;2.3: A common collaborative workflow from GitHub, using fork, clone and pull requests</figcaption><p></p>
 </figure>
 </div>
@@ -706,7 +726,7 @@ <h1 class="title"><span id="sec-vcs" class="quarto-section-identifier d-none d-l
 </ul>
 </div>
   </div>
-</footer><script>var lightboxQuarto = GLightbox({"openEffect":"zoom","selector":".lightbox","loop":true,"descPosition":"bottom","closeEffect":"zoom"});</script>
+</footer><script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","openEffect":"zoom","selector":".lightbox","descPosition":"bottom","loop":true});</script>
 
 
 </body></html>
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diff --git a/docs/chs-command-line/hpc-notions.html b/docs/chs-command-line/hpc-notions.html
index 53c607d..412d7de 100644
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+++ b/docs/chs-command-line/hpc-notions.html
@@ -207,7 +207,7 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">4</span>&nbs
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
   </div>
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       </ul>
@@ -239,12 +239,17 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">4</span>&nbs
   <div class="sidebar-item-container"> 
   <a href="../chs-genomics/functional-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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@@ -252,24 +257,39 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">4</span>&nbs
       <ul id="quarto-sidebar-section-5" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
   </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
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-      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
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         <li class="sidebar-item sidebar-item-section">
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
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-      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">  
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diff --git a/docs/chs-command-line/package-managers.html b/docs/chs-command-line/package-managers.html
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-  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
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   <a href="../chs-genomics/functional-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
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@@ -252,24 +257,39 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">3</span>&nbs
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-  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
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-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
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diff --git a/docs/chs-command-line/welcome-to-command-line.html b/docs/chs-command-line/welcome-to-command-line.html
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-  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
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   <a href="../chs-genomics/functional-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
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         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
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-  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+</li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">
+<li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
   </div>
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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-      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
@@ -352,12 +372,12 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">1</span>&nbs
 </li>
         <li class="sidebar-item sidebar-item-section">
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
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@@ -427,7 +447,7 @@ <h1 class="title"><span id="sec-cli" class="quarto-section-identifier d-none d-l
 <span class="header-section-number">1.1</span> Command line basics</h2>
 <p>Before landing into the CLI let us consider the Unix concept. The first question that comes in this section is: what is Unix? It simply is an <a href="https://en.wikipedia.org/wiki/Operating_system">:operating system (OS)</a>. In other words, it is a set of programs that inter-operate with each other to let you communicate with the machine. A very important variant (or clone) of Unix is the very well known OS <a href="https://en.wikipedia.org/wiki/Linux">:Linux</a>, which was created by <a href="https://en.wikipedia.org/wiki/Linus_Torvalds">:Linus Torvalds</a> from scratch. The most important idea behind Unix based systems is the idea that we can use it to access information and hardware programmatically. Other main feature from Unix-like OS systems is the fact that data is usually stored as text files and the interface by which users communicate with the machine is also text-based (TUI: text user interface as opposed to GUI, graphic user interface).</p>
 <div id="fig-terminal" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-cli/terminal.png" class="lightbox" title="A terminal app displaying common features of the command line interface" data-gallery="quarto-lightbox-gallery-1"><img src="imgs-cli/terminal.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-cli/terminal.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" title="A terminal app displaying common features of the command line interface"><img src="imgs-cli/terminal.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;1.1: A <strong>terminal</strong> app displaying common features of the command line interface</figcaption><p></p>
 </figure>
 </div>
@@ -436,7 +456,7 @@ <h1 class="title"><span id="sec-cli" class="quarto-section-identifier d-none d-l
 <span class="header-section-number">1.1.1</span> File paths</h3>
 <p>Programs, files and directories on every machine (with Unix-like OS) display hierarchical paths (routes), starting out from the <strong>root</strong> (represented by the back-slash character <code>/</code>). The <strong>root</strong> represents the beginning of all the software installed in the machine. And many other files are nested from there forming a tree-like structure for the paths <a href="#fig-tree">Fig.&nbsp;<span>1.2</span></a></p>
 <div id="fig-tree" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-cli/dir-tree.png" class="lightbox" title="A terminal displaying tree-like structure of the programs in a machine with macOS" data-gallery="quarto-lightbox-gallery-2"><img src="imgs-cli/dir-tree.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-cli/dir-tree.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2" title="A terminal displaying tree-like structure of the programs in a machine with macOS"><img src="imgs-cli/dir-tree.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;1.2: A terminal displaying tree-like structure of the programs in a machine with macOS</figcaption><p></p>
 </figure>
 </div>
@@ -510,7 +530,7 @@ <h1 class="title"><span id="sec-cli" class="quarto-section-identifier d-none d-l
 
 <div class="no-row-height column-margin column-container"><div class="">
 <div id="fig-naming-files" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-cli/naming-files.png" class="lightbox" title="Different conventions for naming files or directories as a good computational practice. Such as de the kebab-case or the UpperCammelCase. Illustration by Allison Horst" data-gallery="quarto-lightbox-gallery-3"><img src="imgs-cli/naming-files.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-cli/naming-files.png" class="lightbox" data-gallery="quarto-lightbox-gallery-3" title="Different conventions for naming files or directories as a good computational practice. Such as de the kebab-case or the UpperCammelCase. Illustration by Allison Horst"><img src="imgs-cli/naming-files.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;1.3: Different conventions for naming files or directories as a good computational practice. Such as de the kebab-case or the UpperCammelCase. Illustration by Allison Horst</figcaption><p></p>
 </figure>
 </div>
@@ -550,7 +570,7 @@ <h1 class="title"><span id="sec-cli" class="quarto-section-identifier d-none d-l
 <span class="header-section-number">1.1.3</span> Anatomy of a command</h3>
 <p>There is still many conventions by which the parts of a command line might be called, yet a very standard convention is presented in <a href="#fig-command">Fig.&nbsp;<span>1.4</span></a></p>
 <div id="fig-command" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-cli/command-anatomy.png" class="lightbox" title="A simple command and a convention to call its main components" data-gallery="quarto-lightbox-gallery-4"><img src="imgs-cli/command-anatomy.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-cli/command-anatomy.png" class="lightbox" data-gallery="quarto-lightbox-gallery-4" title="A simple command and a convention to call its main components"><img src="imgs-cli/command-anatomy.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;1.4: A simple command and a convention to call its main components</figcaption><p></p>
 </figure>
 </div>
@@ -569,7 +589,7 @@ <h1 class="title"><span id="sec-cli" class="quarto-section-identifier d-none d-l
 <div class="callout-body-container callout-body">
 <p>Bacterial defense mechanisms to avoid bacteriophage infections are abundant. One of these is the <a href="https://en.wikipedia.org/wiki/Restriction_modification_system">:restriction-modification system (RM-System)</a>, which works by targeting a specific sites called <em>motifs</em>, shared by the phage and bacteria, with methylations. Motifs are commonly represented as a <a href="https://en.wikipedia.org/wiki/Sequence_logo">:sequence logo</a> which is a probabilistic representation of the nucleotides at each position. The challenge consists of finding the number of times the motif from <a href="#fig-motif">Fig.&nbsp;<span>1.5</span></a> appears on <em>B. tequilensis</em> EA-CB0015 genome using a command. Assume that probabilities are equal when multiple bases appeared at one site.</p>
 <div id="fig-motif" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-cli/motif.png" class="lightbox" title="A RM-system motif logo" data-gallery="quarto-lightbox-gallery-5"><img src="imgs-cli/motif.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-cli/motif.png" class="lightbox" data-gallery="quarto-lightbox-gallery-5" title="A RM-system motif logo"><img src="imgs-cli/motif.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;1.5: A RM-system motif logo</figcaption><p></p>
 </figure>
 </div>
@@ -609,14 +629,14 @@ <h1 class="title"><span id="sec-cli" class="quarto-section-identifier d-none d-l
 </div></div><section id="redirection" class="level4" data-number="1.3.3.1"><h4 data-number="1.3.3.1" class="anchored" data-anchor-id="redirection">
 <span class="header-section-number">1.3.3.1</span> Redirection</h4>
 <div class="quarto-figure quarto-figure-center">
-<figure class="figure"><p><a href="imgs-cli/redirection.png" class="lightbox" title="Redirecting flow" data-gallery="quarto-lightbox-gallery-6"><img src="imgs-cli/redirection.png" class="img-fluid figure-img" style="width:70.0%"></a></p>
+<figure class="figure"><p><a href="imgs-cli/redirection.png" class="lightbox" data-gallery="quarto-lightbox-gallery-6" title="Redirecting flow"><img src="imgs-cli/redirection.png" class="img-fluid figure-img" style="width:70.0%"></a></p>
 <p></p><figcaption class="figure-caption">Redirecting flow</figcaption><p></p>
 </figure>
 </div>
 </section><section id="pipe" class="level4 page-columns page-full" data-number="1.3.3.2"><h4 data-number="1.3.3.2" class="anchored" data-anchor-id="pipe">
 <span class="header-section-number">1.3.3.2</span> Pipe</h4>
 <div class="quarto-figure quarto-figure-center">
-<figure class="figure"><p><a href="imgs-cli/pipeflow.png" class="lightbox" title="Pipe flow" data-gallery="quarto-lightbox-gallery-7"><img src="imgs-cli/pipeflow.png" class="img-fluid figure-img" style="width:70.0%"></a></p>
+<figure class="figure"><p><a href="imgs-cli/pipeflow.png" class="lightbox" data-gallery="quarto-lightbox-gallery-7" title="Pipe flow"><img src="imgs-cli/pipeflow.png" class="img-fluid figure-img" style="width:70.0%"></a></p>
 <p></p><figcaption class="figure-caption">Pipe flow</figcaption><p></p>
 </figure>
 </div>
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+</footer><script>var lightboxQuarto = GLightbox({"selector":".lightbox","closeEffect":"zoom","loop":true,"descPosition":"bottom","openEffect":"zoom"});</script>
 
 
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+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true">Sequence analysis</a>
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+  <a href="../chs-sequence-analysis/introduction-to-sequence-analysis.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Sequence analysis</span></a>
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+  <a href="../chs-sequence-analysis/sanger-analysis.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Sanger analysis</span></a>
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+  <a href="../chs-sequence-analysis/sequence-alignments.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Sequence alignments</span></a>
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+  <a href="../chs-sequence-analysis/NGS-TGS-principles.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">NGS and TGS: principles</span></a>
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+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">Phylogenetics</a>
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+  <a href="../chs-phylogenetics/phylogenetic-reconstructions.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Phylogenetics</span></a>
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+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
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+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="true">Genomics</a>
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+  <a href="../chs-genomics/genome-assembly.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Genome assembly</span></a>
+  </div>
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+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/genome-annotation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">12</span>&nbsp; <span class="chapter-title">Genome annotation</span></a>
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+  <a href="../chs-genomics/variant-calling-analysis.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">13</span>&nbsp; <span class="chapter-title">Variant calling analysis</span></a>
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+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/functional-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></a>
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+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link active"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
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+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
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+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
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+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
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+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
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+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
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+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
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+  <a href="../chs-challenges-demos/seq-analysis-challenges.html" class="sidebar-item-text sidebar-link">Seq. Analysis challenges</a>
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+  <li><a href="#whole-genome-comparisons" id="toc-whole-genome-comparisons" class="nav-link" data-scroll-target="#whole-genome-comparisons"><span class="toc-section-number">15.2</span>  Whole genome comparisons</a></li>
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+<h2 data-number="15.1" class="anchored" data-anchor-id="genome-mapping"><span class="header-section-number">15.1</span> Genome mapping</h2>
+</section>
+<section id="whole-genome-comparisons" class="level2" data-number="15.2">
+<h2 data-number="15.2" class="anchored" data-anchor-id="whole-genome-comparisons"><span class="header-section-number">15.2</span> Whole genome comparisons</h2>
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+<script src="https://giscus.app/client.js" data-repo="camilogarciabotero/biocomp-book" data-repo-id="R_kgDOHKOnSw" data-category="General" data-category-id="DIC_kwDOHKOnS84CQ7NN" data-mapping="title" data-reactions-enabled="1" data-emit-metadata="0" data-input-position="top" data-theme="light" data-lang="en" crossorigin="anonymous" async="">
+</script>
+<nav class="page-navigation">
+  <div class="nav-page nav-page-previous">
+      <a href="../chs-genomics/functional-genomics.html" class="pagination-link">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></span>
+      </a>          
+  </div>
+  <div class="nav-page nav-page-next">
+      <a href="../chs-metagenomics/metagenomic-sequencing.html" class="pagination-link">
+        <span class="nav-page-text"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></span> <i class="bi bi-arrow-right-short"></i>
+      </a>
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+</nav>
+</div> <!-- /content -->
+<footer class="footer">
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+    <div class="nav-footer-left">Made with <a href="https://quarto.org/">Quarto</a>. Under <a href="https://github.com/camilogarciabotero/biocomp-book/blob/main/LICENSE">GNU GPL 3.0</a>. Buy me coffee <a href="https://www.paypal.com/paypalme/camilogarciabotero"><i class="fa-solid fa-mug-saucer"></i></a></div>   
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diff --git a/docs/chs-genomics/functional-genomics.html b/docs/chs-genomics/functional-genomics.html
index db46e0b..5af05d9 100644
--- a/docs/chs-genomics/functional-genomics.html
+++ b/docs/chs-genomics/functional-genomics.html
@@ -30,7 +30,7 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
-<link href="../chs-bio-structural/intro-structural-bioinfo.html" rel="next">
+<link href="../chs-genomics/comparative-genomics.html" rel="next">
 <link href="../chs-genomics/variant-calling-analysis.html" rel="prev">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
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 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
   </div>
 </li>
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   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
@@ -252,24 +257,39 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">14</span>&nb
       <ul id="quarto-sidebar-section-5" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
   </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
@@ -284,12 +304,12 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">14</span>&nb
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../HISTORY.html" class="sidebar-item-text sidebar-link">History</a>
@@ -569,8 +589,8 @@ <h2 data-number="14.3" class="anchored" data-anchor-id="kegg-paths"><span class=
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="pagination-link">
-        <span class="nav-page-text"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></span> <i class="bi bi-arrow-right-short"></i>
+      <a href="../chs-genomics/comparative-genomics.html" class="pagination-link">
+        <span class="nav-page-text"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
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diff --git a/docs/chs-genomics/genome-annotation.html b/docs/chs-genomics/genome-annotation.html
index 9b42db3..9fbf687 100644
--- a/docs/chs-genomics/genome-annotation.html
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 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
   </div>
 </li>
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   <a href="../chs-genomics/functional-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
@@ -252,24 +257,39 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">12</span>&nb
       <ul id="quarto-sidebar-section-5" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
   </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
@@ -284,12 +304,12 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">12</span>&nb
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../HISTORY.html" class="sidebar-item-text sidebar-link">History</a>
diff --git a/docs/chs-genomics/genome-assembly.html b/docs/chs-genomics/genome-assembly.html
index 3423868..fbd122e 100644
--- a/docs/chs-genomics/genome-assembly.html
+++ b/docs/chs-genomics/genome-assembly.html
@@ -207,7 +207,7 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">11</span>&nb
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
   </div>
 </li>
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@@ -239,12 +239,17 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">11</span>&nb
   <div class="sidebar-item-container"> 
   <a href="../chs-genomics/functional-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
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+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
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+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
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-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
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-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
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-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
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+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></span>
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diff --git a/docs/chs-genomics/variant-calling-analysis.html b/docs/chs-genomics/variant-calling-analysis.html
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   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
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   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
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+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
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+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
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-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
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-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
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+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../HISTORY.html" class="sidebar-item-text sidebar-link">History</a>
diff --git a/docs/chs-phylogenetics/phylogenetic-reconstructions.html b/docs/chs-phylogenetics/phylogenetic-reconstructions.html
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+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
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+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
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+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
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+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
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+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
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-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
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-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
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+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
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   <a href="../chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
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+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
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           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
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+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
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           <li class="sidebar-item">
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-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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-      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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-      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">  
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@@ -305,13 +326,29 @@ <h1 class="quarto-secondary-nav-title">(Untitled)</h1>
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 </nav>
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-    
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
+        
+    </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
+<header id="title-block-header" class="quarto-title-block default">
+<div class="quarto-title">
+<h1 class="title"><span id="sec-phylogenomics" class="quarto-section-identifier d-none d-lg-block"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></span></h1>
+</div>
 
 
 
+<div class="quarto-title-meta">
+
+    
+    
+  </div>
+  
+
+</header>
+
+
 
 
 </main> <!-- /main -->
diff --git a/docs/chs-sequence-analysis/NGS-TGS-principles.html b/docs/chs-sequence-analysis/NGS-TGS-principles.html
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+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
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   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
       </ul>
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         <li class="sidebar-item sidebar-item-section">
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
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           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
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+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
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       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
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+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
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   <div class="sidebar-item-container"> 
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../HISTORY.html" class="sidebar-item-text sidebar-link">History</a>
diff --git a/docs/chs-sequence-analysis/introduction-to-sequence-analysis.html b/docs/chs-sequence-analysis/introduction-to-sequence-analysis.html
index 7538fee..f8eda76 100644
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-  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
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   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
       </ul>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
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+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+</li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
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+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">
+<li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
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       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
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           </a> 
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-      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
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         <li class="sidebar-item sidebar-item-section">
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
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+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../HISTORY.html" class="sidebar-item-text sidebar-link">History</a>
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+</footer><script>var lightboxQuarto = GLightbox({"descPosition":"bottom","openEffect":"zoom","loop":true,"selector":".lightbox","closeEffect":"zoom"});</script>
 
 
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 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
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   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
       </ul>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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 <li class="sidebar-item">
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+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+</li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">
+<li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
   </div>
 </li>
       </ul>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
@@ -289,12 +309,12 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">6</span>&nbs
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">
+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../HISTORY.html" class="sidebar-item-text sidebar-link">History</a>
@@ -350,14 +370,14 @@ <h1 class="title"><span id="sec-sanger" class="quarto-section-identifier d-none
 <p>Back in 70s there two different methods aiming to determine the base sequences of DNA and they basically operated at the level of base per base reconstruction of the information. The most used during those days was so called <a href="https://en.wikipedia.org/wiki/Maxam%E2%80%93Gilbert_sequencing">:Maxam-Gilbert</a> method and the second one was precisely the chain termination method or dideoxy sequencing or more commonly nowadays <a href="https://en.wikipedia.org/wiki/Sanger_sequencing">:Sanger sequencing</a>. Both methods named after their creators. It was, however the Sanger method the one that gradually became the facto method and continue to be the standard for the next thirty years. In fact, assembled genomes before the 2000s were sequenced with Sanger method, which included the first draft of the Human genome and many other organism <span class="citation" data-cites="brown2018">Brown (<a href="../references.html#ref-brown2018" role="doc-biblioref">2018</a>)</span>.</p>
 
 <div class="no-row-height column-margin column-container"><div id="fig-dna-pol" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-seqan/dna-pol.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" title="A globular structure of a bacterial DNA polymerase"><img src="imgs-seqan/dna-pol.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-seqan/dna-pol.png" class="lightbox" title="A globular structure of a bacterial DNA polymerase" data-gallery="quarto-lightbox-gallery-1"><img src="imgs-seqan/dna-pol.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;6.1: A globular structure of a bacterial DNA polymerase</figcaption><p></p>
 </figure>
 </div></div><section id="the-chain-termination-method" class="level3 page-columns page-full" data-number="6.1.1"><h3 data-number="6.1.1" class="anchored" data-anchor-id="the-chain-termination-method">
 <span class="header-section-number">6.1.1</span> The chain termination method</h3>
 <p>To under stand the chain termination method is important have a clear view of the DNA structure and chemical reaction that enable its polymerization. Whe the</p>
 <div id="fig-dideoxy-reaction" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-seqan/dideoxy-reaction.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2" title="The deoxy-ribose and dideoxy-ribose and consequences on the polymerization of a DNA strand"><img src="imgs-seqan/dideoxy-reaction.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-seqan/dideoxy-reaction.png" class="lightbox" title="The deoxy-ribose and dideoxy-ribose and consequences on the polymerization of a DNA strand" data-gallery="quarto-lightbox-gallery-2"><img src="imgs-seqan/dideoxy-reaction.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;6.2: The deoxy-ribose and dideoxy-ribose and consequences on the polymerization of a DNA strand</figcaption><p></p>
 </figure>
 </div>
@@ -413,7 +433,7 @@ <h1 class="title"><span id="sec-sanger" class="quarto-section-identifier d-none
 </div>
 <p>However the most used file is the binary version <code>AB1</code> which could be red out from different programs including <a href="">cutepeaks</a>. It displays the DNA sequence along with its quality peak in each position <a href="#fig-ab1-trace">Fig.&nbsp;<span>6.4</span></a></p>
 <div id="fig-ab1-trace" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-seqan/ab1-trace.png" class="lightbox" data-gallery="quarto-lightbox-gallery-3" title="A graphic of the AB1 file format from a Sanger sequencing project displayed in cutepeaks software"><img src="imgs-seqan/ab1-trace.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-seqan/ab1-trace.png" class="lightbox" title="A graphic of the AB1 file format from a Sanger sequencing project displayed in cutepeaks software" data-gallery="quarto-lightbox-gallery-3"><img src="imgs-seqan/ab1-trace.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;6.4: A graphic of the <code>AB1</code> file format from a Sanger sequencing project displayed in cutepeaks software</figcaption><p></p>
 </figure>
 </div>
@@ -435,7 +455,7 @@ <h1 class="title"><span id="sec-sanger" class="quarto-section-identifier d-none
 <span class="header-section-number">6.4</span> The 16S rRNA and its relevance for sequencing</h2>
 
 <div class="no-row-height column-margin column-container"><div id="fig-16-rna" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-seqan/16-rRNA.png" class="lightbox" data-gallery="quarto-lightbox-gallery-4" title="Bacillus subtilis subsp. subtilis str. 168 bacterial SSU 16S rRNA"><img src="imgs-seqan/16-rRNA.png" class="img-fluid figure-img" style="width:80.0%"></a></p>
+<figure class="figure"><p><a href="imgs-seqan/16-rRNA.png" class="lightbox" title="Bacillus subtilis subsp. subtilis str. 168 bacterial SSU 16S rRNA" data-gallery="quarto-lightbox-gallery-4"><img src="imgs-seqan/16-rRNA.png" class="img-fluid figure-img" style="width:80.0%"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;6.5: <em>Bacillus subtilis</em> subsp. <em>subtilis</em> str. 168 bacterial SSU 16S rRNA</figcaption><p></p>
 </figure>
 </div></div><div class="callout-warning callout callout-style-default callout-captioned">
@@ -692,7 +712,7 @@ <h1 class="title"><span id="sec-sanger" class="quarto-section-identifier d-none
 </ul>
 </div>
   </div>
-</footer><script>var lightboxQuarto = GLightbox({"openEffect":"zoom","descPosition":"bottom","loop":true,"closeEffect":"zoom","selector":".lightbox"});</script>
+</footer><script>var lightboxQuarto = GLightbox({"openEffect":"zoom","closeEffect":"zoom","loop":true,"selector":".lightbox","descPosition":"bottom"});</script>
 
 
 </body></html>
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@@ -207,7 +207,7 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">7</span>&nbs
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="../chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
   </div>
 </li>
       </ul>
@@ -239,12 +239,17 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">7</span>&nbs
   <div class="sidebar-item-container"> 
   <a href="../chs-genomics/functional-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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@@ -252,24 +257,39 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">7</span>&nbs
       <ul id="quarto-sidebar-section-5" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="../chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="../chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
   </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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-      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
@@ -284,12 +304,12 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">7</span>&nbs
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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-      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../HISTORY.html" class="sidebar-item-text sidebar-link">History</a>
diff --git a/docs/index.html b/docs/index.html
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@@ -215,7 +215,7 @@ <h1 class="quarto-secondary-nav-title">Fundamentals of computational biology</h1
 </li>
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-  <a href="./chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="./chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
   </div>
 </li>
       </ul>
@@ -247,12 +247,17 @@ <h1 class="quarto-secondary-nav-title">Fundamentals of computational biology</h1
   <div class="sidebar-item-container"> 
   <a href="./chs-genomics/functional-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
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@@ -260,24 +265,39 @@ <h1 class="quarto-secondary-nav-title">Fundamentals of computational biology</h1
       <ul id="quarto-sidebar-section-5" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="./chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="./chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
   </div>
 </li>
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   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
@@ -292,12 +312,12 @@ <h1 class="quarto-secondary-nav-title">Fundamentals of computational biology</h1
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
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-      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./HISTORY.html" class="sidebar-item-text sidebar-link">History</a>
diff --git a/docs/intro.html b/docs/intro.html
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+++ b/docs/intro.html
@@ -208,7 +208,7 @@ <h1 class="quarto-secondary-nav-title">Introduction</h1>
 </li>
           <li class="sidebar-item">
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-  <a href="./chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="./chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
   </div>
 </li>
       </ul>
@@ -240,12 +240,17 @@ <h1 class="quarto-secondary-nav-title">Introduction</h1>
   <div class="sidebar-item-container"> 
   <a href="./chs-genomics/functional-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
@@ -253,24 +258,39 @@ <h1 class="quarto-secondary-nav-title">Introduction</h1>
       <ul id="quarto-sidebar-section-5" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="./chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="./chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
   </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
@@ -285,12 +305,12 @@ <h1 class="quarto-secondary-nav-title">Introduction</h1>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./HISTORY.html" class="sidebar-item-text sidebar-link">History</a>
diff --git a/docs/references.html b/docs/references.html
index cdddd1b..b3771df 100644
--- a/docs/references.html
+++ b/docs/references.html
@@ -225,7 +225,7 @@ <h1 class="quarto-secondary-nav-title">References</h1>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">phylogenomics.html</span></a>
+  <a href="./chs-phylogenetics/phylogenomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Phylogenomics</span></a>
   </div>
 </li>
       </ul>
@@ -257,12 +257,17 @@ <h1 class="quarto-secondary-nav-title">References</h1>
   <div class="sidebar-item-container"> 
   <a href="./chs-genomics/functional-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Functional genomics</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./chs-genomics/comparative-genomics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Comparative genomics</span></a>
+  </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Structural bioinformatics</a>
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">Metagenomics</a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
@@ -270,24 +275,39 @@ <h1 class="quarto-secondary-nav-title">References</h1>
       <ul id="quarto-sidebar-section-5" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
+  <a href="./chs-metagenomics/metagenomic-sequencing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Metagenomic sequencing</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Structural bioinformatics</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./chs-bio-structural/intro-structural-bioinfo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Structural bioinformatics</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
+  <a href="./chs-bio-structural/molecular-docking.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Molecular docking</span></a>
   </div>
 </li>
       </ul>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">Challenges</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Challenges</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./chs-challenges-demos/unix-challenges.html" class="sidebar-item-text sidebar-link">Unix challenges</a>
@@ -302,12 +322,12 @@ <h1 class="quarto-secondary-nav-title">References</h1>
   </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">Appendix</a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">Appendix</a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="true">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
-      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth1 show">  
+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./HISTORY.html" class="sidebar-item-text sidebar-link">History</a>
diff --git a/docs/search.json b/docs/search.json
index 4708fea..f40e0a2 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -426,33 +426,40 @@
     "section": "14.3 KEGG paths",
     "text": "14.3 KEGG paths"
   },
+  {
+    "objectID": "chs-genomics/comparative-genomics.html#whole-genome-comparisons",
+    "href": "chs-genomics/comparative-genomics.html#whole-genome-comparisons",
+    "title": "15  Comparative genomics",
+    "section": "15.2 Whole genome comparisons",
+    "text": "15.2 Whole genome comparisons\nmummer mauve mmseq"
+  },
   {
     "objectID": "chs-bio-structural/intro-structural-bioinfo.html",
     "href": "chs-bio-structural/intro-structural-bioinfo.html",
-    "title": "15  Structural bioinformatics",
+    "title": "17  Structural bioinformatics",
     "section": "",
     "text": "Structural bioinformatics is a multidisciplinary area enriched by chemistry, physics, computer science and many others. Although, it could be focused on different biological macro-molecules, here the emphasis will be focused on proteins.\nOne of the first protein structure elucidated was myoglobin and it triggered the study of the role of the structure of proteins and its biological functions\nIdentify a protein related to your study that could be further analyzed."
   },
   {
     "objectID": "chs-bio-structural/intro-structural-bioinfo.html#protein-structures",
     "href": "chs-bio-structural/intro-structural-bioinfo.html#protein-structures",
-    "title": "15  Structural bioinformatics",
-    "section": "15.1 Protein structures",
-    "text": "15.1 Protein structures\nDifference between the levels of protein structure primary structure is the basic linear representation of aminoacids. Natural aminoacids and modified or rare aminoacids display physico-chemical rich information and could be represented by letters. Therefore in the genetic code we could find the one-letter code.\nSecondary structures result from the spatial arrangement of aminoacids that interact with each closer neighbors. There are some remarkable secondary structures such as \\(\\beta\\)-sheets, \\(\\alpha\\)-helix, coils (flexible) and others.\nTertiary structure informs about the structural disposition of the secondary structures that fold between each other due to hydrophobic interactions, disulfure bonds, and other chemical interactions forming a globular and dynamic structure. Thus, proteins could display multiple structural states depending on the physical and energy stability (see the :Levinthal’s paradox).\nQuaternary structures result from interaction of multiple tertiary structures. The structure, therefore dictates the protein function. This basic concept have triggered more recently a boom on the analysis of the structure of proteins."
+    "title": "17  Structural bioinformatics",
+    "section": "17.1 Protein structures",
+    "text": "17.1 Protein structures\nDifference between the levels of protein structure primary structure is the basic linear representation of aminoacids. Natural aminoacids and modified or rare aminoacids display physico-chemical rich information and could be represented by letters. Therefore in the genetic code we could find the one-letter code.\nSecondary structures result from the spatial arrangement of aminoacids that interact with each closer neighbors. There are some remarkable secondary structures such as \\(\\beta\\)-sheets, \\(\\alpha\\)-helix, coils (flexible) and others.\nTertiary structure informs about the structural disposition of the secondary structures that fold between each other due to hydrophobic interactions, disulfure bonds, and other chemical interactions forming a globular and dynamic structure. Thus, proteins could display multiple structural states depending on the physical and energy stability (see the :Levinthal’s paradox).\nQuaternary structures result from interaction of multiple tertiary structures. The structure, therefore dictates the protein function. This basic concept have triggered more recently a boom on the analysis of the structure of proteins."
   },
   {
     "objectID": "chs-bio-structural/intro-structural-bioinfo.html#identifying-or-predicting-protein-structures",
     "href": "chs-bio-structural/intro-structural-bioinfo.html#identifying-or-predicting-protein-structures",
-    "title": "15  Structural bioinformatics",
-    "section": "15.2 Identifying or predicting protein structures",
-    "text": "15.2 Identifying or predicting protein structures\nXray crystallography, nuclear magnetic resonance (NMR) allows to encapsulated dynamic information of the protein in time Electron micrography (EM) and Cryo-EM. These experiment rely on highly specialized set ups and there are other drawbacks.\nTo date, helium is scarce around the world, so labs all around are having trouble to get this element.\nModelling the structure whether ab initio or by homology also allow structure prediction. However these strategies\nRecently AlphaFold\nThe protein database (PDB)\nProtein topologies resulting from the folding: horshoe, beta-barrel and other could be identified\nStructural classification of proteins (SCOP) when analyzing a new protein classification by class, architecture, topology (fold-family), homologous superfamily and sequence family\nImportance of Gene Ontology\n\n15.2.1 Secondary structure prediction\nSecondary structures could also be represented in one letter (e.g.)\nFunctional domains could be predicted by sequence alignment and allow structural inference. Main predictions are based heavily on machine learning and are frequently accepted under a consensus of multiple tools.\nThere is a group of protein called intrinsically-disordered proteins that change in its tertiary structures quite frequently, therefore it prediction could be troublesome.\n\n\n\n\n\n\nExercise 01\n\n\n\nSubmit 5lWM (JAK3) from the PDB on FASTA format on the JPRED and PSIPRED and compared with the experimentally predicted version of the protein. Analyze the predictions and tell are there differences between predictions? Which one is more accurate?"
+    "title": "17  Structural bioinformatics",
+    "section": "17.2 Identifying or predicting protein structures",
+    "text": "17.2 Identifying or predicting protein structures\nXray crystallography, nuclear magnetic resonance (NMR) allows to encapsulated dynamic information of the protein in time Electron micrography (EM) and Cryo-EM. These experiment rely on highly specialized set ups and there are other drawbacks.\nTo date, helium is scarce around the world, so labs all around are having trouble to get this element.\nModelling the structure whether ab initio or by homology also allow structure prediction. However these strategies\nRecently AlphaFold\nThe protein database (PDB)\nProtein topologies resulting from the folding: horshoe, beta-barrel and other could be identified\nStructural classification of proteins (SCOP) when analyzing a new protein classification by class, architecture, topology (fold-family), homologous superfamily and sequence family\nImportance of Gene Ontology\n\n17.2.1 Secondary structure prediction\nSecondary structures could also be represented in one letter (e.g.)\nFunctional domains could be predicted by sequence alignment and allow structural inference. Main predictions are based heavily on machine learning and are frequently accepted under a consensus of multiple tools.\nThere is a group of protein called intrinsically-disordered proteins that change in its tertiary structures quite frequently, therefore it prediction could be troublesome.\n\n\n\n\n\n\nExercise 01\n\n\n\nSubmit 5lWM (JAK3) from the PDB on FASTA format on the JPRED and PSIPRED and compared with the experimentally predicted version of the protein. Analyze the predictions and tell are there differences between predictions? Which one is more accurate?"
   },
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     "objectID": "chs-bio-structural/intro-structural-bioinfo.html#pdb-database-introduction",
     "href": "chs-bio-structural/intro-structural-bioinfo.html#pdb-database-introduction",
-    "title": "15  Structural bioinformatics",
-    "section": "15.3 PDB database introduction",
-    "text": "15.3 PDB database introduction\nThe PDB database is one of the most important and ancient open biological database where all new protein structures are submitted. It is an international consortium where several regions work together to curate information.\nThe PDB in Europe (PDBe) is not only for proteins but form many other experimentally predicted macro-molecules (protein-protein interactions, peptides, RNA and so on).\nProtein structures are registered using a unique code of four characters.\nX-ray crystallography: is a chemical state of the macro-molecule where it is immobilized, therefore information correspond to one state of the structure, then crystal protein is submitted to an x-ray beam to generate a diffraction pattern.\nNMR spectroscopy: captures dynamic information of the protein, but generally resolves small proteins. The principle?\nElectron microscopy adapted to cryo-preservation allow proteins visualization."
+    "title": "17  Structural bioinformatics",
+    "section": "17.3 PDB database introduction",
+    "text": "17.3 PDB database introduction\nThe PDB database is one of the most important and ancient open biological database where all new protein structures are submitted. It is an international consortium where several regions work together to curate information.\nThe PDB in Europe (PDBe) is not only for proteins but form many other experimentally predicted macro-molecules (protein-protein interactions, peptides, RNA and so on).\nProtein structures are registered using a unique code of four characters.\nX-ray crystallography: is a chemical state of the macro-molecule where it is immobilized, therefore information correspond to one state of the structure, then crystal protein is submitted to an x-ray beam to generate a diffraction pattern.\nNMR spectroscopy: captures dynamic information of the protein, but generally resolves small proteins. The principle?\nElectron microscopy adapted to cryo-preservation allow proteins visualization."
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     "objectID": "chs-challenges-demos/unix-challenges.html",
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