Auspice fork from github of https://github.com/urbanslug/auspice
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<!DOCTYPE html><html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>Displaying mutliple trees · Auspice</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="Auspice has the ability to display two trees side-by-side, and to draw lines between tips with the same name (aka tanglegrams)."/><meta name="docsearch:language" content="en"/><meta property="og:title" content="Displaying mutliple trees · Auspice"/><meta property="og:type" content="website"/><meta property="og:url" content="https://nextstrain.github.io/auspice/"/><meta property="og:description" content="Auspice has the ability to display two trees side-by-side, and to draw lines between tips with the same name (aka tanglegrams)."/><meta property="og:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><meta name="twitter:card" content="summary"/><meta name="twitter:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><link rel="shortcut icon" href="/auspice/img/favicon.ico"/><link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/solarized-dark.min.css"/><script type="text/javascript" src="https://buttons.github.io/buttons.js"></script><script src="/auspice/js/scrollSpy.js"></script><link rel="stylesheet" href="/auspice/css/main.css"/><script src="/auspice/js/codetabs.js"></script></head><body class="sideNavVisible separateOnPageNav"><div class="fixedHeaderContainer"><div class="headerWrapper wrapper"><header><a href="/auspice/"><img class="logo" src="/auspice/img/logo-light.svg" alt="Auspice"/><h2 class="headerTitleWithLogo">Auspice</h2></a><div class="navigationWrapper navigationSlider"><nav class="slidingNav"><ul class="nav-site nav-site-internal"><li class="siteNavGroupActive"><a href="/auspice/introduction/overview" target="_self">Docs</a></li></ul></nav></div></header></div></div><div class="navPusher"><div class="docMainWrapper wrapper"><div class="docsNavContainer" id="docsNav"><nav class="toc"><div class="toggleNav"><section class="navWrapper wrapper"><div class="navBreadcrumb wrapper"><div class="navToggle" id="navToggler"><div class="hamburger-menu"><div class="line1"></div><div class="line2"></div><div class="line3"></div></div></div><h2><i></i><span>Advanced Functionality</span></h2><div class="tocToggler" id="tocToggler"><i class="icon-toc"></i></div></div><div class="navGroups"><div class="navGroup"><h3 class="navGroupCategoryTitle">Introduction</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/introduction/overview">Overview</a></li><li class="navListItem"><a class="navItem" href="/auspice/introduction/install">Install Auspice</a></li><li class="navListItem"><a class="navItem" href="/auspice/introduction/how-to-run">How to Run Auspice</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Advanced Functionality</h3><ul class=""><li class="navListItem navListItemActive"><a class="navItem" href="/auspice/advanced-functionality/second-trees">Displaying mutliple trees</a></li><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/misc">Miscellaneous</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Customising Auspice</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/customise-client/introduction">Customising Auspice</a></li><li class="navListItem"><a class="navItem" href="/auspice/customise-client/api">Client Customisation API</a></li><li class="navListItem"><a class="navItem" href="/auspice/customise-client/requests">Requests Made from the Client</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Using a Custom Server</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/server/introduction">Auspice servers</a></li><li class="navListItem"><a class="navItem" href="/auspice/server/api">Server API</a></li><li class="navListItem"><a class="navItem" href="/auspice/server/authentication">Authentication</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Narratives</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/narratives/introduction">Communicating Results Using Narratives</a></li><li class="navListItem"><a class="navItem" href="/auspice/narratives/how-to-write">Writing a Narrative</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Release Notes</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/releases/changelog">Changelog</a></li><li class="navListItem"><a class="navItem" href="/auspice/releases/v2">Auspice Version 2.0</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Contributing</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/contributing/overview">Contributing</a></li></ul></div></div></section></div><script>
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</script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">Displaying mutliple trees</h1></header><article><div><span><p>Auspice has the ability to display two trees side-by-side, and to draw lines between tips with the same name (aka tanglegrams).
This is useful to compare the shape of different trees, especially when they are from the same organism -- for instance comparing phylogenies constructed from different
segments of the same influenza virus can tell you a lot about the different histories of the segments which have the capacity to reassort (see image below).</p>
<h2><a class="anchor" aria-hidden="true" id="how-to-load-multiple-trees"></a><a href="#how-to-load-multiple-trees" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>How to load multiple trees</h2>
<p>You can compare any two datasets which you have available -- for instance if you had &quot;flu/seasonal/h3n2/ha/2y&quot; and &quot;flu/seasonal/h3n2/na/2y&quot; then loading the URL &quot;flu/seasonal/h3n2/ha/2y:flu/seasonal/h3n2/na/2y&quot; would load them both.
A toggle is made available in the sidebar to turn off the lines drawn between tips.</p>
<p><img src="/auspice/assets/tangle.png" alt="two-trees">
<em>Comparing epitope mutations between HA and NA (worldwide influena H3N2).</em>
<em>Notice how the segments can differ drastically in how many epitope mutations they acquire!</em>
<em>While the crossing of the lines between the tips doesn't always prove reassortment, it's usually a good indication that reassortment is present.</em></p>
<h2><a class="anchor" aria-hidden="true" id="showing-potential-datasets-in-the-sidebar"></a><a href="#showing-potential-datasets-in-the-sidebar" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Showing potential datasets in the sidebar</h2>
<p>Depending on the way you've labelled your datasets, potential second trees are available in a sidebar dropdown.
These are defined by the <a href="/auspice/server/api#charon-getavailable">getAvailable API request</a>.
Currently, the logic in <code>auspice view</code> is to match all datasets which:</p>
<ul>
<li>contain the same first &quot;part&quot; of the URL -- interpreted here to represent the same pathogen.</li>
<li>have the same number of &quot;parts&quot; in the URL (parts are delimited by a <code>_</code> in the filename or a <code>/</code> in the URL).</li>
<li>differ from the currently selected dataset by only 1 part.</li>
</ul>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/how-to-run"><span class="arrow-prev"></span><span>How to Run Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/misc"><span>Miscellaneous</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-load-multiple-trees">How to load multiple trees</a></li><li><a href="#showing-potential-datasets-in-the-sidebar">Showing potential datasets in the sidebar</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>