@@ -1,7 +1,7 @@

 Package: ggtree

 Type: Package

 Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

-Version: 1.5.17

+Version: 1.7.0

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.

@@ -1,3 +1,7 @@

+CHANGES IN VERSION 1.6.0

+------------------------

+ o BioC 3.4 released <2016-10-18, Tue>

+ 

 CHANGES IN VERSION 1.5.17

 ------------------------

  o read.nhx support newick file <2016-10-17, Mon>

@@ -1,9 +1,9 @@

 ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

 ===========================================================================================================================

-[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.20-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.17-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-15283/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.20-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.0-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-15283/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--10--17-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--10--18-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)

@@ -17,7 +17,7 @@ Please cite the following article when using `ggtree`:

 **G Yu**, 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. ***Methods in Ecology and Evolution***. *accepted*

-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-187-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-195-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

 ------------------------------------------------------------------------

@@ -107,6 +107,12 @@

+<li >

+    <a href="../emojifont/">emojifont</a>

+</li>

+

+                    

+                        

 <li >

     <a href="../ggtree/">ggtree</a>

 </li>

@@ -107,6 +107,12 @@

+<li >

+    <a href="../emojifont/">emojifont</a>

+</li>

+

+                    

+                        

 <li >

     <a href="../ggtree/">ggtree</a>

 </li>

@@ -149,7 +155,7 @@

                     </a>

                 </li>

                 <li >

-                    <a rel="prev" href="../ggtree/">

+                    <a rel="prev" href="../emojifont/">

                         Next <i class="fa fa-arrow-right"></i>

                     </a>

                 </li>

@@ -107,6 +107,12 @@

+<li >

+    <a href="../emojifont/">emojifont</a>

+</li>

+

+                    

+                        

 <li >

     <a href="../ggtree/">ggtree</a>

 </li>

@@ -107,6 +107,12 @@

+<li >

+    <a href="../emojifont/">emojifont</a>

+</li>

+

+                    

+                        

 <li >

     <a href="../ggtree/">ggtree</a>

 </li>

@@ -107,6 +107,12 @@

+<li >

+    <a href="../emojifont/">emojifont</a>

+</li>

+

+                    

+                        

 <li >

     <a href="../ggtree/">ggtree</a>

 </li>

@@ -107,6 +107,12 @@

+<li >

+    <a href="../emojifont/">emojifont</a>

+</li>

+

+                    

+                        

 <li >

     <a href="../ggtree/">ggtree</a>

 </li>

new file mode 100644

@@ -0,0 +1,228 @@

+<!DOCTYPE html>

+<html lang="en">

+    <head>

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\ No newline at end of file

@@ -107,6 +107,12 @@

+<li >

+    <a href="../emojifont/">emojifont</a>

+</li>

+

+                    

+                        

 <li >

     <a href="../ggtree/">ggtree</a>

 </li>

@@ -107,6 +107,12 @@

+<li >

+    <a href="../emojifont/">emojifont</a>

+</li>

+

+                    

+                        

 <li >

     <a href="../ggtree/">ggtree</a>

 </li>

@@ -217,11 +223,11 @@

   }  

   </style>

-<div id = 'chart43167772f4ca' class = 'rChart morris'></div>

+<div id = 'chart737bca330a' class = 'rChart morris'></div>

 <script type='text/javascript'>

     var chartParams = {

- "element": "chart43167772f4ca",

+ "element": "chart737bca330a",

 "width":            800,

 "height":            400,

 "xkey": "year",

@@ -235,7 +241,7 @@

 "pubid": "HtEfBTGE9r8C" 

 } 

 ],

-"id": "chart43167772f4ca",

+"id": "chart737bca330a",

 "labels": "cites" 

 },

       chartType = "Bar"

@@ -107,6 +107,12 @@

+<li >

+    <a href="../emojifont/">emojifont</a>

+</li>

+

+                    

+                        

 <li class="active">

     <a href="./">ggtree</a>

 </li>

@@ -144,7 +150,7 @@

                     </a>

                 </li>

                 <li >

-                    <a rel="next" href="../DOSE/">

+                    <a rel="next" href="../emojifont/">

                         <i class="fa fa-arrow-left"></i> Previous

                     </a>

                 </li>

@@ -107,6 +107,12 @@

+<li >

+    <a href="emojifont/">emojifont</a>

+</li>

+

+                    

+                        

 <li >

     <a href="ggtree/">ggtree</a>

 </li>

@@ -227,7 +233,7 @@

 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>

 <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>

-<a href="https://github.com/GuangchuangYu/ggtree"><img alt="develVersion" src="https://img.shields.io/badge/devel%20version-1.5.17-blue.svg?style=flat" /></a>

+<a href="https://github.com/GuangchuangYu/ggtree"><img alt="develVersion" src="https://img.shields.io/badge/devel%20version-1.7.0-blue.svg?style=flat" /></a>

 <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-15283/total-blue.svg?style=flat" /></a>

 <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="month" src="https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat" /></a></p>

 <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.

@@ -238,7 +244,7 @@

 <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&amp;hl=en&amp;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-189-blue.svg?style=flat" /></a></p>

+<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-195-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>

@@ -107,6 +107,12 @@

+<li >

+    <a href="../emojifont/">emojifont</a>

+</li>

+

+                    

+                        

 <li >

     <a href="../ggtree/">ggtree</a>

 </li>

@@ -192,7 +192,7 @@

         }, 

         {

             "location": "/featuredArticles/", 

-            "text": "Let us know if you have published using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart43167772f4ca\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart43167772f4ca\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape\n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens\n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015\n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species\n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976", 

+            "text": "Let us know if you have published using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart737bca330a\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart737bca330a\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape\n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens\n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015\n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species\n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976", 

             "title": "Featured Articles"

         }, 

         {

@@ -220,6 +220,11 @@

             "text": "", 

             "title": "DOSE"

         }, 

+        {

+            "location": "/emojifont/", 

+            "text": "", 

+            "title": "emojifont"

+        }, 

         {

             "location": "/ggtree/", 

             "text": "", 

@@ -4,7 +4,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/</loc>

-     <lastmod>2016-10-17</lastmod>

+     <lastmod>2016-10-18</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -12,7 +12,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/documentation/</loc>

-     <lastmod>2016-10-17</lastmod>

+     <lastmod>2016-10-18</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -20,7 +20,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/faq/</loc>

-     <lastmod>2016-10-17</lastmod>

+     <lastmod>2016-10-18</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -28,7 +28,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/featuredArticles/</loc>

-     <lastmod>2016-10-17</lastmod>

+     <lastmod>2016-10-18</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -37,43 +37,49 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/ChIPseeker/</loc>

-     <lastmod>2016-10-17</lastmod>

+     <lastmod>2016-10-18</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/clusterProfiler/</loc>

-     <lastmod>2016-10-17</lastmod>

+     <lastmod>2016-10-18</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/DOSE/</loc>

-     <lastmod>2016-10-17</lastmod>

+     <lastmod>2016-10-18</lastmod>

+     <changefreq>daily</changefreq>

+    </url>

+        

+    <url>

+     <loc>https://guangchuangyu.github.io/ggtree/emojifont/</loc>

+     <lastmod>2016-10-18</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/ggtree/</loc>

-     <lastmod>2016-10-17</lastmod>

+     <lastmod>2016-10-18</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/GOSemSim/</loc>

-     <lastmod>2016-10-17</lastmod>

+     <lastmod>2016-10-18</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/meshes/</loc>

-     <lastmod>2016-10-17</lastmod>

+     <lastmod>2016-10-18</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/ReactomePA/</loc>

-     <lastmod>2016-10-17</lastmod>

+     <lastmod>2016-10-18</lastmod>

      <changefreq>daily</changefreq>

     </url>

new file mode 120000

@@ -0,0 +1 @@

+../mysoftware/emojifont.md

\ No newline at end of file

@@ -36,10 +36,10 @@ Let us know if you have published using `ggtree` and your publication will be fe

   }  

   </style>

-<div id = 'chart43167772f4ca' class = 'rChart morris'></div>

+<div id = 'chart737bca330a' class = 'rChart morris'></div>

 <script type='text/javascript'>

     var chartParams = {

- "element": "chart43167772f4ca",

+ "element": "chart737bca330a",

 "width":            800,

 "height":            400,

 "xkey": "year",

@@ -53,7 +53,7 @@ Let us know if you have published using `ggtree` and your publication will be fe

 "pubid": "HtEfBTGE9r8C" 

 } 

 ],

-"id": "chart43167772f4ca",

+"id": "chart737bca330a",

 "labels": "cites" 

 },

       chartType = "Bar"

@@ -16,7 +16,7 @@

 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">

 [![releaseVersion](https://img.shields.io/badge/release%20version-1.4.20-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)

-[![develVersion](https://img.shields.io/badge/devel%20version-1.5.17-blue.svg?style=flat)](https://github.com/GuangchuangYu/ggtree)

+[![develVersion](https://img.shields.io/badge/devel%20version-1.7.0-blue.svg?style=flat)](https://github.com/GuangchuangYu/ggtree)

 [![total](https://img.shields.io/badge/downloads-15283/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

 [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

@@ -35,7 +35,7 @@ Please cite the following article when using `ggtree`:

 [![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628)

 [![citation](https://img.shields.io/badge/cited%20by-1-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)

-[![Altmetric](https://img.shields.io/badge/Altmetric-189-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)

+[![Altmetric](https://img.shields.io/badge/Altmetric-195-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)

 __G Yu__, 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. __*Methods in Ecology and Evolution*__. *accepted*.