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<li class="main active"><a href="#vignettes"> Vignettes</a></li>
<li class="main "><a href="#blog-posts"> Blog posts</a></li>
<li><a href="#news-and-updates"> News and updates</a></li>
<li><a href="#data-manipulation"> Data manipulation</a></li>
<li><a href="#tree-visualization"> Tree visualization</a></li>
<li><a href="#tree-annotation"> Tree annotation</a></li>
<li><a href="#tree-manipulation"> Tree manipulation</a></li>
<li><a href="#application"> Application</a></li>
<li><a href="#funny-stuff"> Funny stuff</a></li>
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<h2 id="vignettes"><i class="fa fa-book"></i> Vignettes</h2>
<ul>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtree.html">ggtree</a></li>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeImport.html">Tree Data Import</a></li>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeVisualization.html">Tree Visualization</a></li>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeAnnotation.html">Tree Annotation</a></li>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeManipulation.html">Tree Manipulation</a></li>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/advanceTreeAnnotation.html">Advance Tree Annotation</a></li>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtreeUtilities.html">ggtree utilities</a></li>
</ul>
<h2 id="blog-posts"><i class="fa fa-wordpress"></i> Blog posts</h2>
<h3 id="news-and-updates"><i class="fa fa-angle-double-right"></i> News and updates</h3>
<ul>
<li><a href="https://guangchuangyu.github.io/2014/12/viewing-and-annotating-phylogenetic-tree-with-ggtree">viewing and annotating phylogenetic tree with ggtree</a></li>
<li><a href="https://guangchuangyu.github.io/2015/01/ggtree-in-bioconductor-3.1">ggtree in Bioconductor 3.1</a></li>
<li><a href="https://guangchuangyu.github.io/2015/04/news-of-my-bioc-packages">BioC 3.1: NEWS of my BioC packages</a></li>
<li><a href="https://guangchuangyu.github.io/2015/10/news-of-my-bioc-packages">BioC 3.2: NEWS of my BioC packages</a></li>
<li><a href="https://guangchuangyu.github.io/2015/12/news-of-ggtree">News of ggtree</a></li>
<li><a href="https://guangchuangyu.github.io/2016/05/news-of-my-bioc-packages">BioC 3.3: NEWS of my BioC packages</a></li>
<li><a href="https://guangchuangyu.github.io/2016/08/ggtree-paper-published">ggtree paper published</a></li>
</ul>
<h3 id="data-manipulation"><i class="fa fa-angle-double-right"></i> Data manipulation</h3>
<ul>
<li><a href="https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree">subsetting data in ggtree</a></li>
<li><a href="https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format">ggtree supports phylip tree format</a></li>
</ul>
<h3 id="tree-visualization"><i class="fa fa-angle-double-right"></i> Tree visualization</h3>
<ul>
<li><a href="https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/">ggtree - updating a tree view</a></li>
<li><a href="https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree">an example of drawing beast tree using ggtree</a></li>
</ul>
<h3 id="tree-annotation"><i class="fa fa-angle-double-right"></i> Tree annotation</h3>
<ul>
<li><a href="https://guangchuangyu.github.io/2016/01/label-edge-number-in-ggtree">label edge number in ggtree</a></li>
<li><a href="https://guangchuangyu.github.io/2015/08/subview">subview</a></li>
<li><a href="https://guangchuangyu.github.io/2016/01/annotate-a-phylogenetic-tree-with-insets">Annotate a phylogenetic tree with insets</a></li>
<li><a href="https://guangchuangyu.github.io/2015/08/ggtree-annotate-phylogenetic-tree-with-local-images">ggtree annotate phylogenetic tree with local images</a></li>
<li><a href="https://guangchuangyu.github.io/2016/03/embed-images-in-ggplot2-via-subview-and-annotate-a-phylogenetic-tree-with-images-using-inset-function">embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function</a></li>
<li><a href="https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree">identify method for ggtree</a></li>
</ul>
<h3 id="tree-manipulation"><i class="fa fa-angle-double-right"></i> Tree manipulation</h3>
<ul>
<li><a href="https://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree">flip and rotate branches in ggtree</a></li>
</ul>
<h3 id="application"><i class="fa fa-angle-double-right"></i> Application</h3>
<ul>
<li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/">ggtree for microbiome data</a></li>
<li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-outbreak-data/">ggtree for outbreak data</a></li>
<li><a href="https://github.com/GuangchuangYu/plotTree-ggtree">ggtree version of plotTree.R</a></li>
</ul>
<h3 id="funny-stuff"><i class="fa fa-angle-double-right"></i> Funny stuff</h3>
<ul>
<li><a href="https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts">ggtree with funny fonts</a></li>
<li><a href="https://guangchuangyu.github.io/2015/09/comic-phylogenetic-tree-with-ggtree-and-comicr">comic phylogenetic tree with ggtree and comicR</a></li>
<li><a href="https://guangchuangyu.github.io/2015/12/use-emoji-font-in-r">use emoji font in R</a></li>
</ul>
<h3 id="users-feedback"><i class="fa fa-angle-double-right"></i> User's feedback</h3>
<ul>
<li><a href="https://guangchuangyu.github.io/2016/02/tweets-of-ggtree">tweets of ggtree</a></li>
<li>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>
</ul>
<p><i class="fa fa-hand-o-right"></i> Find out more on <a href="https://guangchuangyu.github.io/tags/ggtree/">https://guangchuangyu.github.io/tags/ggtree/</a>.</p>
<h2 id="slides"><i class="fa fa-slideshare"></i> Slides</h2>
<ul>
<li><a href="https://guangchuangyu.github.io/presentation/2014-ggplot2/">Generating publication quality figures using R & ggplot2</a></li>
<li><a href="https://guangchuangyu.github.io/presentation/2016-ggtree-chinar/">ggtree for visualization and annotation of phylogenetic trees</a></li>
</ul>
<h2 id="video"><i class="fa fa-youtube-play"></i> Video</h2>
<ul>
<li><a href="https://www.youtube.com/watch?v=KcF8Ec38mzI">interactive clade highlighting</a></li>
<li><a href="https://www.youtube.com/watch?v=lKNn4QlPO0E">interactive rotating clades</a></li>
<li><a href="https://www.youtube.com/watch?v=SmcceRD_jxg">interactive clade labeling</a></li>
</ul>
<h2 id="workflow"><i class="fa fa-gift"></i> Workflow</h2>
<ul>
<li><a href="https://rpubs.com/gutijosh9430/124817">recreate a tree from a publication (<strong>Bloom</strong> <em>et al</em>, <strong><em>Science</em></strong> 2010)</a></li>
</ul></div>
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