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<li class="main "><a href="#featured-articles"> Featured Articles</a></li>
<li class="main "><a href="#installation"> Installation</a></li>
<li class="main "><a href="#overview"> Overview</a></li>
<li><a href="#getting-tree-into-r"> Getting tree into R</a></li>
<li><a href="#tree-visualization-annotation"> Tree visualization & annotation</a></li>
<li><a href="#tree-manipulation"> Tree manipulation</a></li>
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<p><a href="https://bioconductor.org/packages/ggtree"><img alt="releaseVersion" src="https://img.shields.io/badge/release%20version-1.4.20-blue.svg?style=flat" /></a>
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<p>The <code>ggtree</code> package extending the <code>ggplot2</code> package. It based on grammar of graphics and takes all the good parts of <code>ggplot2</code>. <code>ggtree</code> is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.
<code>ggtree</code> 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>
<h2 id="authors"><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>
<h2 id="citation"><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 alt="doi" src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a>
<a href="https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-1-blue.svg?style=flat" /></a>
<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-188-blue.svg?style=flat" /></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>. <em>accepted</em>.</p>
<h2 id="featured-articles"><i class="fa fa-pencil"></i> Featured Articles</h2>
<p><img alt="" src="https://guangchuangyu.github.io/featured_img/ggtree/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg" /></p>
<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>
<h2 id="installation"><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><code class="r">## 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>
<h2 id="overview"><i class="fa fa-cogs"></i> Overview</h2>
<h4 id="getting-tree-into-r"><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>
<h4 id="tree-visualization-annotation"><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>
<h4 id="tree-manipulation"><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>
<h2 id="projects-that-depend-on-ggtree"><i class="fa fa-code-fork"></i> Projects that depend on <em>ggtree</em></h2>
<h4 id="bioconductor-packages"><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/philr">philr</a>: Phylogenetic partitioning based ILR transform for metagenomics data</li>
</ul>
<h4 id="other-applications"><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>
<h2 id="feedback"><i class="fa fa-comments"></i> Feedback</h2>
<p><ul class="fa-ul">
<li><i class="fa-li fa fa-hand-o-right"></i> Please make sure you <a href="https://guangchuangyu.github.io/2016/07/how-to-bug-author/">follow the guide</a> before posting any issue/question</li>
<li><i class="fa-li fa fa-bug"></i> For bugs or feature requests, please post to <i class="fa fa-github-alt"></i> <a href="https://github.com/GuangchuangYu/ggtree/issues">github issue</a></li>
<li><i class="fa-li fa fa-question"></i> For user questions, please post to <i class="fa fa-google"></i> <a href="https://groups.google.com/forum/#!forum/bioc-ggtree">google group</a></li>
<li><i class="fa-li fa fa-support"></i> We are also following every post tagged with <strong>ggtree</strong> on <a href="https://support.bioconductor.org/">Bioconductor support site</a> and <a href="https://www.biostars.org/">Biostars</a></li>
<li><i class="fa-li fa fa-commenting"></i> Join the group chat on <a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a> and <a href="http://huati.weibo.com/k/ggtree"><i class="fa fa-weibo fa-lg"></i></a></li>
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