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Separate intro slides.

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trvrb committed Apr 26, 2016
1 parent 88bf1ac commit 24de902cddb62ce78ec13ac522a7050d36ee134c
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## Viral phylodynamics
* [Introduction](http://bedford.io/projects/phylodynamics-lecture/intro.html): These slides give an introduction to what is meant by phylodynamics.
* [Influenza](http://bedford.io/projects/phylodynamics-lecture/flu.html): These slides describe influenza dynamics and antigenic evolution.
* [The Coalescent](http://bedford.io/projects/phylodynamics-lecture/coalescent.html): These slides introduce the coalescent, demographic inference and selection.
* [Phylogenetics](http://bedford.io/projects/phylodynamics-lecture/phylogenetics.html): These slides introduce phylogenetic inference via parsimony, maximum likelihood and Bayesian approaches.
* [Phylogenetics](http://bedford.io/projects/phylodynamics-lecture/phylogenetics.html): These slides introduce phylogenetic inference via parsimony, maximum likelihood and Bayesian approaches.
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<head>
<meta charset="utf-8">
<title>Viral phylodynamics</title>
<title>The coalescent</title>
<meta name="author" content="Trevor Bedford">
@@ -36,63 +36,6 @@
<!-- Any section element inside of this container is displayed as a slide -->
<div class="slides">
<section data-background="#5097BA">
<h2 class="title">Phylogenies</h2>
</section>
<section>
<h3>Phylogenies describe history</h3>
<img class="stretch" src="images/phylogenies_tudors.jpg">
</section>
<section>
<h3>Phylogenies describe history</h3>
<img class="stretch" src="images/phylogenies_haeckel.jpg">
<div class="citation">
Haeckel 1879
</div>
</section>
<section>
<h3>Phylogenies describe history</h3>
<img class="stretch" src="images/phylogenies_pace.png">
<div class="citation">
<a href="http://www.sciencemag.org/content/276/5313/734.short">Pace 1997</a>
</div>
</section>
<section>
<h3>Phylogenies reveal process</h3>
<img class="stretch" src="images/phylogenies_darwin.png">
<div class="citation">
Darwin 1859
</div>
</section>
<section data-background="#5BA6A7">
<h2 class="title">Epidemic process</h2>
</section>
<section data-transition="none">
<h3>Epidemic process</h3>
<img class="stretch" src="images/infection_tree_1.png">
</section>
<section data-transition="none">
<h3>Sample some individuals</h3>
<img class="stretch" src="images/infection_tree_2.png">
</section>
<section data-transition="none">
<h3>Sequence and determine phylogeny</h3>
<img class="stretch" src="images/infection_tree_3.png">
</section>
<section data-transition="none">
<h3>Sequence and determine phylogeny</h3>
<img class="stretch" src="images/infection_tree_4.png">
</section>
<section data-background="#69B091">
<h2 class="title">The coalescent</h2>
Binary file not shown.
Binary file not shown.
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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Viral phylodynamics</title>
<meta name="author" content="Trevor Bedford">
<meta name="apple-mobile-web-app-capable" content="yes" />
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
<link rel="stylesheet" href="reveal/css/reveal.min.css">
<link rel="stylesheet" href="reveal/css/theme/trvrb.css" id="theme">
<link rel="stylesheet" href="reveal/css/font-awesome/css/font-awesome.min.css">
<!-- For syntax highlighting -->
<link rel="stylesheet" href="reveal/lib/css/zenburn.css">
</head>
<body>
<div style="position: absolute; top:10px; left:10px; z-index:100;">
<a href="http://bedford.io/projects/phylodynamics-lecture/">
<i class="fa fa-times-circle" style="color: #bbb;"></i>
</a>
</div>
<div class="reveal">
<!-- Color ramp: ["#5097BA", "#5BA6A7", "#69B091", "#79B77D", "#8BBB6A", "#9EBE5A", "#B2BD4D", "#C4B945", "#D4B13F", "#DFA43B"] -->
<!-- Any section element inside of this container is displayed as a slide -->
<div class="slides">
<section data-background="#5097BA">
<h2 class="title">Phylogenies</h2>
</section>
<section>
<h3>Phylogenies describe history</h3>
<img class="stretch" src="images/phylogenies_tudors.jpg">
</section>
<section>
<h3>Phylogenies describe history</h3>
<img class="stretch" src="images/phylogenies_haeckel.jpg">
<div class="citation">
Haeckel 1879
</div>
</section>
<section>
<h3>Phylogenies describe history</h3>
<img class="stretch" src="images/phylogenies_pace.png">
<div class="citation">
<a href="http://www.sciencemag.org/content/276/5313/734.short">Pace 1997</a>
</div>
</section>
<section>
<h3>Phylogenies reveal process</h3>
<img class="stretch" src="images/phylogenies_darwin.png">
<div class="citation">
Darwin 1859
</div>
</section>
<section data-background="#5BA6A7">
<h2 class="title">Epidemic process</h2>
</section>
<section data-transition="none">
<h3>Epidemic process</h3>
<img class="stretch" src="images/infection_tree_1.png">
</section>
<section data-transition="none">
<h3>Sample some individuals</h3>
<img class="stretch" src="images/infection_tree_2.png">
</section>
<section data-transition="none">
<h3>Sequence and determine phylogeny</h3>
<img class="stretch" src="images/infection_tree_3.png">
</section>
<section data-transition="none">
<h3>Sequence and determine phylogeny</h3>
<img class="stretch" src="images/infection_tree_4.png">
</section>
<section>
<h3>Localized Middle Eastern MERS-CoV phylogeny</h3>
<img class="stretch" src="images/pathogen_phylogeny_mers.jpg">
<div class="citation">
<a href="http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(13)61887-5/abstract">Cotten et al 2013</a>
</div>
</section>
<section>
<h3>Regional West African Ebola phylogeny</h3>
<img class="stretch" src="images/pathogen_phylogeny_ebola.png">
<div class="citation">
<a href="http://bedford.io/papers/park-ebola-transmission/">Park et al 2015</a>
</div>
</section>
<section>
<h3>Global influenza phylogeny</h3>
<img class="stretch" src="images/pathogen_phylogeny_flu.png">
<div class="citation">
<a href="http://bedford.io/papers/bedford-global-circulation/">Bedford et al 2015</a>
</div>
</section>
</div>
</div>
<script src="reveal/lib/js/head.min.js"></script>
<script src="reveal/js/reveal.min.js"></script>
<script src="reveal/js/config.js"></script>
</body>
</html>

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