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learn.html
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---
layout: page
title: Learn
description: Videos, tutorials and articles about tree sequences.
permalink: /learn/
---
<!-- START: hero-type-2 -->
<div class="hero hero--type-2">
<div class="container">
<div class="row">
<div class="col-md-8 col-lg-6">
<h2 id="what-is" class="hero__heading">
What is a tree sequence?
</h2>
<div class="hero__content wysiwyg">
<p>
A <em>succinct tree sequence</em>, or tree sequence for short, represents the relationships
between a set of DNA sequences. Tree sequences can be used to store genetic data
efficiently, and enable powerful analysis of millions of whole genomes at a time. They
can be created by simulation or by inferring relationships from genetic variation.
</p>
</div>
</div>
</div>
</div>
</div>
<!-- END: hero-type-2 -->
<!-- START: cards-type-2 -->
<section class="section section--cards section--cards--type-2">
<div class="container">
<div class="row">
<div class="col-md-8">
<h3 class="section__heading">
Tree sequences provide:
</h3>
</div>
</div>
<div class="row">
<div class="col-lg-4">
<!-- START: card -->
<a href="{{ 'tutorials/what_is.html#sec-what-is-ancestry' | relative_url }}" class="card card--type-2">
<h4 id="genetic-ancestry" class="card__heading">
A full record of genetic ancestry
</h4>
<p class="card__text">
A tree sequence concisely captures the full history of a set of genomes by sharing
common branches between adjacent genetic trees
</p>
<span class="list__item__link link link--type-1">
<span class="link__text">
Read more
</span>
</span>
</a>
<!-- END: card -->
</div>
<div class="col-lg-4">
<!-- START: card -->
<a href="{{ 'tutorials/what_is.html#sec-what-is-dna-data' | relative_url }}" class="card card--type-2">
<h4 id="DNA-encoding" class="card__heading">
An encoding of DNA data
</h4>
<p class="card__text">
Placing mutations on a tree sequence allows lossless representation and compression of
DNA datasets
</p>
<span class="list__item__link link link--type-1">
<span class="link__text">
Read more
</span>
</span>
</a>
<!-- END: card -->
</div>
<div class="col-lg-4">
<!-- START: card -->
<a href="{{ 'tutorials/what_is.html#sec-what-is-analysis' | relative_url }}" class="card card--type-2">
<h4 id="efficient-analysis" class="card__heading">
An efficient analysis framework
</h4>
<p class="card__text">
Many of the analyses we perform on DNA data can be expressed naturally as operations on
the ancestral trees, leading to highly efficient algorithms
</p>
<span class="list__item__link link link--type-1">
<span class="link__text">
Read more
</span>
</span>
</a>
<!-- END: card -->
</div>
</div>
</div>
</section>
<!-- END: cards-type-2 -->
<!-- START: filters -->
<section class="section section--filters">
<div class="container">
<div class="row">
<div class="col-md-8">
<h3 id="tutorials-publications-videos" class="section__heading">
Browse tutorials, publications and videos:
</h3>
</div>
</div>
<div class="row">
<div class="col">
<div class="btn-group" role="group" aria-label="Filters">
<a data-r-selector="all" onclick="switch_filter('all')" class="btn btn-outline-primary active" aria-current="page">All</a>
<a data-r-selector="paper" onclick="switch_filter('paper')" class="btn btn-outline-primary">Publications</a>
<a data-r-selector="tutorial" onclick="switch_filter('tutorial')" class="btn btn-outline-primary">Tutorials</a>
<a data-r-selector="video" onclick="switch_filter('video')" class="btn btn-outline-primary">Videos</a>
<!-- <a onclick="switch_filter" class="btn btn-outline-primary">Applications</a>-->
</div>
</div>
</div>
<!-- <div class="row">-->
<!-- <div class="col-md-8 col-lg-5">-->
<!-- <select class="form-select form-select-lg">-->
<!-- <option>Choose resource type</option>-->
<!-- <option value="publication">publication</option>-->
<!-- <option value="tutorial">tutorial</option>-->
<!-- <option value="video">video</option>-->
<!-- </select>-->
<!-- </div>-->
<!-- </div>-->
</div>
<div class="container">
<div class="row">
{% assign resources = site.resources | sort: "timestamp" | reverse %}
{% for r in resources %}
<div class="col-lg-4" data-r-type="{{r.type}}">
<!-- START: card -->
<div class="card card--type-3">
<div class="card__metadata">
<span class="card__category">{{r.type | capitalize}}</span>
</div>
<h5 class="card__heading">
{{r.title}}
</h5>
{% if r.type == "paper" %}
<div class="wysiwyg">
<p>
{{ r.timestamp | date: "%d %B, %Y" }}
</p>
<p>
{{ r.journal }} ({{ r.year }}) {{ r.author }}
</p>
<p>
doi: <a href="https://doi.org/{{ r.doi }}">{{ r.doi }}</a>
</p>
<p>
{{r.content}}
</p>
</div>
<a href="https://doi.org/{{r.doi}}" class="list__item__link link link--type-1 link--type-1--external"
target="_blank"
rel="noopener noreferrer">
<span class="link__text">
Read the article
</span>
</a>
{% endif %}
{% if r.type == "video" %}
<div class="wysiwyg">
<p>
{{ r.timestamp | date: "%d %B, %Y" }}
</p>
<p>
{{ r.who }} at {{ r.where }}</br>
{{ r.content }}
</p>
</div>
{% if r.youtube-id %}
<a href="https://www.youtube.com/watch?v={{r.youtube-id}}" class="video-trigger"
data-bs-toggle="modal" data-bs-target="#globalModal" data-video-id="{{r.youtube-id}}"
data-video-aspect-ratio="16x9">
<span class="visually-hidden">
Play video
</span>
<div class="video-trigger__image-wrapper">
<img alt="video thumbnail" class="img-fluid"
src="https://img.youtube.com/vi/{{r.youtube-id | split: "&" | first }}/maxresdefault.jpg">
</div>
</a>
{% elsif r.vimeo-id %}
<!-- Vimeo embeds don't work with out a code from the video creator, so just link-->
<a href="https://www.vimeo.com/{{r.vimeo-id}}" class="video-trigger">
<span class="visually-hidden">
Play video
</span>
<div class="video-trigger__image-wrapper">
<img alt="video thumbnail" class="img-fluid"
src="{{r.thumbnail}}">
</div>
</a>
{% endif %}
{% endif %}
{% if r.type == "tutorial" %}
<div class="wysiwyg">
<p>
{{ r.timestamp | date: "%d %B, %Y" }}
</p>
<p> {{ r.content }} </p>
</div>
<a
{% if r.url_override %}
href={{ r.url_override }}
{% else %}
href={{ '/tutorials/' | append: r.tutorial_id | append: '.html' | relative_url }}
{% endif %}
class="list__item__link link link--type-1 link--type-1--external"
target="_blank"
rel="noopener noreferrer">
<span class="link__text">
See the tutorial
</span>
</a>
{% endif %}
<!-- <div class="card__metadata">-->
<!-- <span class="card__tag">Population genetics</span>-->
<!-- </div>-->
</div>
<!-- END: card -->
</div>
{% endfor %}
</div>
</div>
<!-- START: pagination -->
<div class="container" style="display: none">
<div class="row">
<div class="col">
<nav class="pagination-wrapper">
<ul class="pagination list list--unstyled list--horizontal">
<li class="list__item">
<span class="pagination__number pagination__number--prev disabled">
Prev
</span>
</li>
<li class="list__item">
<span class="pagination__number pagination__number--current">
1
</span>
</li>
<li class="list__item">
<a class="pagination__number" href="#">
2
</a>
</li>
<li class="list__item">
<a class="pagination__number" href="#">
3
</a>
</li>
<li class="list__item">
<a class="pagination__number" href="#">
4
</a>
</li>
<li class="list__item">
<span class="pagination__dots">
…
</span>
</li>
<li class="list__item">
<a class="pagination__number" href="#">
12
</a>
</li>
<li class="list__item">
<a class="pagination__number pagination__number--next" href="#">
Next
</a>
</li>
</ul>
</nav>
</div>
</div>
</div>
<!-- END: pagination -->
</section>
<!-- END: cards-type-3 -->