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(This article was first published on <strong><a href="https://guangchuangyu.github.io/2016/08/ggtree-paper-published"> R on Guangchuang YU</a></strong>, and kindly contributed to <a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers)</a> </div>
<p>Today <a target="_blank" href="https://guangchuangyu.github.io/ggtree"><code>ggtree</code></a> received <a target="_blank" href="https://github.com/GuangchuangYu/ggtree/stargazers">100 stars</a> on <i></i> and I found the paper was <a target="_blank" href="http://dx.doi.org/10.1111/2041-210X.12628">online</a> at the same day by the tweet:</p>
<blockquote class="twitter-tweet"><p dir="ltr" lang="ja">ggtree, Methods in Ecology and Evolutionに掲載されたのか。オープンアクセスっぽいな。<a target="_blank" href="https://t.co/JlET18BSZv">https://t.co/JlET18BSZv</a></p>
<p>— ホクソピペット (@siero5335) <a target="_blank" href="https://twitter.com/siero5335/status/765521239146233856">August 16, 2016</a></p></blockquote>
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<p>I am quite exciting about it. Now ggtree is citable by doi:<a target="_blank" href="http://dx.doi.org/10.1111/2041-210X.12628"><code>10.1111/2041-210X.12628</code></a>.</p>
<p>In the review period, <code>ggtree</code> had already been cited by several papers:</p>
<p><code>1</code>. <a target="_blank" href="https://doi.org/10.7717/peerj.976">https://doi.org/10.7717/peerj.976</a></p>
<p>Annotating phylogenetic tree with image files (i.e. secondary structure).</p>
<p><img alt="" src="https://i0.wp.com/guangchuangyu.github.io/ggtree/featured_img/2015_peerJ_fig-9-2x.jpg?w=456&ssl=1" data-recalc-dims="1"></p>
<p><code>2</code>. <a target="_blank" href="http://dx.doi.org/10.1016/j.meegid.2015.12.006">http://dx.doi.org/10.1016/j.meegid.2015.12.006</a></p>
<p>Highlight clades and annotate phylogenetic tree with genotype table.</p>
<p><img alt="" src="https://i1.wp.com/guangchuangyu.github.io/ggtree/featured_img/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg?w=456&ssl=1" data-recalc-dims="1"></p>
<p><code>3</code>. <a target="_blank" href="http://dx.doi.org/10.3389%2Ffcimb.2016.00036">http://dx.doi.org/10.3389%2Ffcimb.2016.00036</a></p>
<p>Annotate phylogenetic tree with binary matrix.</p>
<p><img alt="" src="https://i1.wp.com/guangchuangyu.github.io/ggtree/featured_img/2016_fcimb-06-00036-g003.jpg?w=456&ssl=1" data-recalc-dims="1"></p>
<p><code>4</code>. <a target="_blank" href="http:/%E2%80%8B/%E2%80%8Bdx.%E2%80%8Bdoi.%E2%80%8Borg/%E2%80%8B10.%E2%80%8B1104/%E2%80%8Bpp.%E2%80%8B16.%E2%80%8B00359">http:/​/​dx.​doi.​org/​10.​1104/​pp.​16.​00359</a></p>
<p>Annotate phylogenetic tree with sequence features.</p>
<p><img alt="" src="https://i2.wp.com/guangchuangyu.github.io/ggtree/featured_img/2016_PlantPhysiology.png?w=456&ssl=1" data-recalc-dims="1"></p>
<p><code>5</code>. <a target="_blank" href="http://dx.doi.org/10.1101/067207">http://dx.doi.org/10.1101/067207</a></p>
<p>Annotate with bootstrap values.</p>
<p><img alt="" src="https://i1.wp.com/cloud.githubusercontent.com/assets/626539/17700401/273895c6-63f8-11e6-91da-7431b78b22af.png?w=456&ssl=1" data-recalc-dims="1"></p>
<p><code>6</code>. <a target="_blank" href="http://www.nature.com/articles/srep30158">http://www.nature.com/articles/srep30158</a></p>
<p>Visualize bootstrap value infer by RAxML and phyml on the same tree.</p>
<p><img alt="" src="https://i1.wp.com/cloud.githubusercontent.com/assets/626539/17127143/de15b7c0-5335-11e6-8621-edce0e581308.png?w=456&ssl=1" data-recalc-dims="1"></p>
<p><code>7</code>. <a target="_blank" href="http://dx.doi.org/10.1101/053371">http://dx.doi.org/10.1101/053371</a></p>
<p><code>8</code>. <a target="_blank" href="http://dx.doi.org/10.1105/tpc.16.00053">http://dx.doi.org/10.1105/tpc.16.00053</a></p>
<p><code>9</code>. <a target="_blank" href="http://dx.doi.org/10.1111/mec.13474">http://dx.doi.org/10.1111/mec.13474</a></p>
<p><code>10</code>. <a target="_blank" href="http://dx.doi.org/10.1371/journal.pone.0160958">http://dx.doi.org/10.1371/journal.pone.0160958</a></p>
<p><code>11</code>. <a target="_blank" href="http://dx.doi.org/10.1111/2041-210X.12593">http://dx.doi.org/10.1111/2041-210X.12593</a></p>
<p><code>12</code>. <a target="_blank" href="http://dx.doi.org/10.1101/053371">http://dx.doi.org/10.1101/053371</a></p>
<p>The <a target="_blank" href="http://dx.doi.org/10.1111/2041-210X.12628">ggtree paper</a> provides several comprehensive and reproducible examples. It can be a good reference for complex tree annotation. <a target="_blank" href="https://guangchuangyu.github.io/presentation/2016-ggtree-chinar/">My slides</a> in 9<sup>th</sup> China R conference summarized the functionalities that <code>ggtree</code> provided.</p>
<p>More information can be found in <a target="_blank" href="https://guangchuangyu.github.io/ggtree">ggtree homepage</a>. Hope you have fun with <code>ggtree</code>.</p>
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