index.html

---
title: population-scale genomics
layout: default
description: Tskit-dev - An open-source software ecosystem using tree sequences for efficient and scalable genomics.
---
<div class="page-wrapper home">

    <!-- START: header -->
    <header class="header">
        <!-- START: navbar -->
        {% include navbar.html %}
        <!-- END: navbar -->

        <!-- START: heading -->
        <div class="page-heading">
            <div class="container">
                <div class="row">
                    <div class="col">
                        <h1 class="page-heading__text">
                            <span class="page-heading__text__highlight">Population-scale</span> genomics
                        </h1>
                    </div>
                </div>
            </div>
        </div>
        <!-- END: heading -->
    </header>
    <!-- END: header -->

    <!-- START: content -->
    <main class="page-content" id="content">
        <!-- START: hero-type-1 -->
        <div class="hero hero--type-1">
            <div class="container">
                <div class="row">
                    <div class="col-md-8 col-lg-6">
                        <h2 class="hero__heading">
                            tskit for genetics research
                        </h2>
                        <div class="hero__content wysiwyg">
                            <p>
                                Tskit enables performant storage, manipulation and analysis of genomes and phylogenies
                                using
                                succinct tree sequences usable from Python, C and R. Other software programs use tskit,
                                forming an interoperating ecosystem of tools.
                            </p>
                            <p>
                                This site is a collection of resources to help you <a href="{{ '/learn' | relative_url }}">learn about tree
                                sequences</a> and
                                <a href="{{ '/software' | relative_url }}">associated software</a>, and help you join the <a href="{{ '/community' | relative_url }}">online
                                community</a> of open source developers
                                that makes it all possible.
                            </p>
                        </div>
                    </div>
                </div>
            </div>
        </div>
        <!-- END: hero-type-1 -->

        <!-- START: call-to-action-type-1 -->
        <section class="section section--call-to-action call-to-action call-to-action--type-1">
            <div class="container">
                <div class="row">
                    <div class="col-lg-10 offset-lg-1">
                        <div class="call-to-action__content">
                            <h3 class="call-to-action__heading">
                                New to tskit?
                            </h3>
                            <p class="call-to-action__text">
                                Find out how tskit can help you in your research
                            </p>
                            <a href="{{ '/genetics-research' | relative_url }}" class="btn btn--type-1">
                                Discover
                            </a>
                        </div>
                    </div>
                </div>
            </div>
        </section>
        <!-- END: call-to-action-type-1 -->

        <!-- START: cards-type-1 -->
        <section class="section section--cards section--cards--type-1">
            <div class="container">
                <div class="row">
                    <div class="col-md-8">
                        <h2 class="section__heading">
                            Looking for tskit software?
                        </h2>
                    </div>
                </div>
                <div class="row">
                    <div class="col-lg-4">
                        <!-- START: card -->
                        <div class="card">
                            <h3 class="card__heading">
                                Simulate
                            </h3>
                            {% assign sims = site.software | where: "category","simulate" %}
                            {% for app in sims %}
                            <a href="{{ app.url | relative_url}}" class="list__item__link link link--type-1 link--type-1--size-1">
                                <span class="link__text">
                                    {{ app.name }}
                                </span>
                            </a>
                            {% endfor %}
                        </div>
                        <!-- END: card -->
                    </div>
                    <div class="col-lg-4">
                        <!-- START: card -->
                        <div class="card">
                            <h3 class="card__heading">
                                Analyse
                            </h3>
                            {% assign sims = site.software | where: "category","analyse" %}
                            {% for app in sims %}
                            <a href="{{ app.url | relative_url}}" class="list__item__link link link--type-1 link--type-1--size-1">
                                <span class="link__text">
                                    {{ app.name }}
                                </span>
                            </a>
                            {% endfor %}
                        </div>
                        <!-- END: card -->
                    </div>
                    <div class="col-lg-4">
                        <!-- START: card -->
                        <div class="card">
                            <h3 class="card__heading">
                                Infer
                            </h3>
                            {% assign sims = site.software | where: "category","infer" %}
                            {% for app in sims %}
                            <a href="{{ app.url | relative_url}}" class="list__item__link link link--type-1 link--type-1--size-1">
                                <span class="link__text">
                                    {{ app.name }}
                                </span>
                            </a>
                            {% endfor %}
                        </div>
                        <!-- END: card -->
                    </div>
                </div>
            </div>
        </section>
        <!-- END: cards -->

        <!-- START: icon-links-list -->
        <section class="section section--icon-links-list">
            <div class="container">
                <div class="row">
                    <div class="col-md-8">
                        <h2 class="section__heading">
                            See how tskit applies to your research
                        </h2>
                    </div>
                </div>
                <div class="row section__position-anchor">
                    <!-- NOTE: Don't change these column values, it'll break the icon positioning! -->
                    <div class="col-md-6 offset-md-5">
                        <ul class="list list--unstyled">
                            <li class="list__item">
                                <a href="{{ '/genetics-research/#popgen' | relative_url}}" class="link link--type-1 link--type-1--size-1 link--type-1--bg-1">
                                    <span class="link__text">
                                        Population genetics research
                                    </span>
                                </a>
                                <!-- START: icon-population-genetics-research -->
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                            </li>
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                                <a href="{{ '/genetics-research/#statgen' | relative_url}}" class="link link--type-1 link--type-1--size-1 link--type-1--bg-1">
                                    <span class="link__text">
                                        Statistical genetics research
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                            </li>
                            <li class="list__item">
                                <a href="{{ '/genetics-research/#phylogen' | relative_url}}" class="link link--type-1 link--type-1--size-1 link--type-1--bg-1">
                                    <span class="link__text">
                                        Phylogenetics
                                    </span>
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