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<h1>ggtree: visualization and annotation of phylogenetic trees </h1>
<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>
<p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.3-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-17742/total-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-834/month-blue.svg?style=flat" /></a></p>
<p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em> is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. <em>ggtree</em> is released within the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor</a> project and the source code is hosted on <a href="https://github.com/GuangchuangYu/ggtree"><i class="fa fa-github fa-lg"></i> GitHub</a>.</p>
<div id="authors" class="section level2">
<h2><i class="fa fa-user"></i> Authors</h2>
<p>Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</p>
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<div id="citation" class="section level2">
<h2><i class="fa fa-book"></i> Citation</h2>
<p>Please cite the following article when using <code>ggtree</code>:</p>
<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-347-blue.svg?style=flat" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-30-blue.svg?style=flat" alt="citation" /></a></p>
<p><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. <strong><em>Methods in Ecology and Evolution</em></strong>. 2017, 8(1):28-36.</p>
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<h2><i class="fa fa-pencil"></i> Featured Articles</h2>
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<p><i class="fa fa-hand-o-right"></i> Find out more on <i class="fa fa-pencil"></i> <a href="https://guangchuangyu.github.io/ggtree/featuredArticles/">Featured Articles</a>.</p>
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<div id="installation" class="section level2">
<h2><i class="fa fa-download"></i> Installation</h2>
<p>Install <code>ggtree</code> is easy, follow the guide on the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor page</a>:</p>
<pre class="r"><code>## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
## biocLite("BiocUpgrade") ## you may need this
biocLite("ggtree")</code></pre>
<p>If you have problems when installing some of the dependent packages, please refer to the <a href="https://github.com/GuangchuangYu/ggtree/wiki/ggtree-installation">ggtree-installation</a> wiki page.</p>
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<div id="overview" class="section level2">
<h2><i class="fa fa-cogs"></i> Overview</h2>
<div id="getting-tree-into-r" class="section level4">
<h4><i class="fa fa-angle-double-right"></i> Getting tree into R</h4>
<ul>
<li>tree parsers: bring evolution evidences to be used/analyzed in <code>R</code></li>
<li><code>merge_tree</code>: allows evolution evidences to be merged and compared</li>
<li><code>fortify</code> methods: convert tree objects into tidy data frame</li>
</ul>
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<div id="tree-visualization-annotation" class="section level4">
<h4><i class="fa fa-angle-double-right"></i> Tree visualization & annotation</h4>
<ul>
<li>parsing tree as a collection of nodes allows grammar of graphics to be supported</li>
<li><code>geom_tree</code>: extends <code>ggplot2</code> to support tree structure</li>
<li>several layers and functions for tree annotation</li>
<li>supports annotating phylogenetic trees with user’s own data</li>
</ul>
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<div id="tree-manipulation" class="section level4">
<h4><i class="fa fa-angle-double-right"></i> Tree manipulation</h4>
<ul>
<li>helper functions for tree manipulation, make it possible to explore the tree visually</li>
</ul>
<p><i class="fa fa-hand-o-right"></i> Find out details and examples on <i class="fa fa-book"></i> <a href="https://guangchuangyu.github.io/ggtree/documentation/">Documentation</a>.</p>
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<div id="projects-that-depend-on-ggtree" class="section level2">
<h2><i class="fa fa-code-fork"></i> Projects that depend on <em>ggtree</em></h2>
<div id="cran-packages" class="section level4">
<h4><i class="fa fa-angle-double-right"></i> CRAN packages</h4>
<ul>
<li><a href="https://cran.r-project.org/package=harrietr">harrietr</a>: Wrangle Phylogenetic Distance Matrices and Other Utilities</li>
</ul>
</div>
<div id="bioconductor-packages" class="section level4">
<h4><i class="fa fa-angle-double-right"></i> Bioconductor packages</h4>
<ul>
<li><a href="https://www.bioconductor.org/packages/LINC">LINC</a>: co-expression of lincRNAs and protein-coding genes</li>
<li><a href="https://www.bioconductor.org/packages/LymphoSeq">LymphoSeq</a>: Analyze high-throughput sequencing of T and B cell receptors</li>
<li><a href="https://www.bioconductor.org/packages/philr">philr</a>: Phylogenetic partitioning based ILR transform for metagenomics data</li>
</ul>
</div>
<div id="other-applications" class="section level4">
<h4><i class="fa fa-angle-double-right"></i> Other applications</h4>
<ul>
<li><a href="https://bitbucket.org/biobakery/breadcrumbs">BreadCrumbs</a>: Collection of scripts for metagenomics analysis</li>
<li><a href="https://github.com/esnapd/DegeneratePrimerTools">DegeneratePrimerTools</a>: Utilities for Creating and Validating Degenerate primers</li>
<li><a href="https://github.com/olli0601/phyloscan">phyloscan</a>: scan phylogenies created along a genome for patterns</li>
</ul>
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