@@ -1,15 +1,15 @@

 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-1.5.14-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-13439/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1122/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-1.5.14-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-13544/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1122/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--09--22-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--09--26-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)

 The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.

-[![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ggtree.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract)

+[![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ggtree.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)

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

@@ -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-166-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-167-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

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

@@ -50,7 +50,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/

 ### Download stats

-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-13439/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1122/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-13544/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1122/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

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

          |                                                                               *             |

@@ -83,6 +83,51 @@

                 </li>

+            

+                <li class="dropdown">

+                    <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a>

+                    <ul class="dropdown-menu">

+                    

+                        

+<li >

+    <a href="../mysoftware/ChIPseeker/">ChIPseeker</a>

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/clusterProfiler/">clusterProfiler</a>

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/DOSE/">DOSE</a>

+</li>

+

+                    

+                        

+<li >

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

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/GOSemSim/">GOSemSim</a>

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/ReactomePA/">ReactomePA</a>

+</li>

+

+                    

+                    </ul>

+                </li>

+            

+            

             </ul>

             <!-- Search, Navigation and Repo links -->

@@ -83,6 +83,51 @@

                 </li>

+            

+                <li class="dropdown">

+                    <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a>

+                    <ul class="dropdown-menu">

+                    

+                        

+<li >

+    <a href="../mysoftware/ChIPseeker/">ChIPseeker</a>

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/clusterProfiler/">clusterProfiler</a>

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/DOSE/">DOSE</a>

+</li>

+

+                    

+                        

+<li >

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

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/GOSemSim/">GOSemSim</a>

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/ReactomePA/">ReactomePA</a>

+</li>

+

+                    

+                    </ul>

+                </li>

+            

+            

             </ul>

             <!-- Search, Navigation and Repo links -->

@@ -83,6 +83,51 @@

                 </li>

+            

+                <li class="dropdown">

+                    <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a>

+                    <ul class="dropdown-menu">

+                    

+                        

+<li >

+    <a href="../mysoftware/ChIPseeker/">ChIPseeker</a>

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/clusterProfiler/">clusterProfiler</a>

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/DOSE/">DOSE</a>

+</li>

+

+                    

+                        

+<li >

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

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/GOSemSim/">GOSemSim</a>

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/ReactomePA/">ReactomePA</a>

+</li>

+

+                    

+                    </ul>

+                </li>

+            

+            

             </ul>

             <!-- Search, Navigation and Repo links -->

@@ -97,8 +142,8 @@

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

                     </a>

                 </li>

-                <li class="disabled">

-                    <a rel="prev" >

+                <li >

+                    <a rel="prev" href="../mysoftware/ChIPseeker/">

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

                     </a>

                 </li>

@@ -166,11 +211,11 @@

   }  

   </style>

-<div id = 'chart10275e5014cf' class = 'rChart morris'></div>

+<div id = 'chart16f2218d1abb' class = 'rChart morris'></div>

 <script type='text/javascript'>

     var chartParams = {

- "element": "chart10275e5014cf",

+ "element": "chart16f2218d1abb",

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@@ -184,7 +229,7 @@

 "pubid": "HtEfBTGE9r8C" 

 } 

 ],

-"id": "chart10275e5014cf",

+"id": "chart16f2218d1abb",

 "labels": "cites" 

 },

       chartType = "Bar"

@@ -83,6 +83,51 @@

                 </li>

+            

+                <li class="dropdown">

+                    <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a>

+                    <ul class="dropdown-menu">

+                    

+                        

+<li >

+    <a href="../mysoftware/ChIPseeker/">ChIPseeker</a>

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/clusterProfiler/">clusterProfiler</a>

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/DOSE/">DOSE</a>

+</li>

+

+                    

+                        

+<li >

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

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/GOSemSim/">GOSemSim</a>

+</li>

+

+                    

+                        

+<li >

+    <a href="../mysoftware/ReactomePA/">ReactomePA</a>

+</li>

+

+                    

+                    </ul>

+                </li>

+            

+            

             </ul>

             <!-- Search, Navigation and Repo links -->

@@ -177,7 +222,7 @@

 <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-1.5.14-blue.svg?style=flat" /></a>

-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-13439/total-blue.svg?style=flat" /></a>

+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-13544/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-1122/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.

 <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>

@@ -187,7 +232,7 @@

 <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-166-blue.svg?style=flat" /></a></p>

+<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-167-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="./featured_img/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg" /></p>

@@ -182,7 +182,7 @@

         }, 

         {

             "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\": \"chart10275e5014cf\",\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\": \"chart10275e5014cf\",\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\": \"chart16f2218d1abb\",\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\": \"chart16f2218d1abb\",\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"

         }, 

         {

@@ -194,6 +194,36 @@

             "location": "/featuredArticles/#2015", 

             "text": "The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens   Molecuar Ecology  Dec. 2015  http://dx.doi.org/10.1111/mec.13474   Genetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015   Infection, Genetics and Evolution  Dec. 2015  http://dx.doi.org/10.1016/j.meegid.2015.12.006   Trans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species   PeerJ  May 2015  https://doi.org/10.7717/peerj.976", 

             "title": " 2015"

+        }, 

+        {

+            "location": "/../mysoftware/ChIPseeker/", 

+            "text": "", 

+            "title": "ChIPseeker"

+        }, 

+        {

+            "location": "/../mysoftware/clusterProfiler/", 

+            "text": "", 

+            "title": "clusterProfiler"

+        }, 

+        {

+            "location": "/../mysoftware/DOSE/", 

+            "text": "", 

+            "title": "DOSE"

+        }, 

+        {

+            "location": "/../mysoftware/ggtree/", 

+            "text": "", 

+            "title": "ggtree"

+        }, 

+        {

+            "location": "/../mysoftware/GOSemSim/", 

+            "text": "", 

+            "title": "GOSemSim"

+        }, 

+        {

+            "location": "/../mysoftware/ReactomePA/", 

+            "text": "", 

+            "title": "ReactomePA"

         }

     ]

 }

\ No newline at end of file

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

     <url>

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

-     <lastmod>2016-09-22</lastmod>

+     <lastmod>2016-09-26</lastmod>

      <changefreq>daily</changefreq>

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

     <url>

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

-     <lastmod>2016-09-22</lastmod>

+     <lastmod>2016-09-26</lastmod>

      <changefreq>daily</changefreq>

     </url>

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

     <url>

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

-     <lastmod>2016-09-22</lastmod>

+     <lastmod>2016-09-26</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -28,9 +28,49 @@

     <url>

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

-     <lastmod>2016-09-22</lastmod>

+     <lastmod>2016-09-26</lastmod>

      <changefreq>daily</changefreq>

     </url>

+    

+        

+    <url>

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

+     <lastmod>2016-09-26</lastmod>

+     <changefreq>daily</changefreq>

+    </url>

+        

+    <url>

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

+     <lastmod>2016-09-26</lastmod>

+     <changefreq>daily</changefreq>

+    </url>

+        

+    <url>

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

+     <lastmod>2016-09-26</lastmod>

+     <changefreq>daily</changefreq>

+    </url>

+        

+    <url>

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

+     <lastmod>2016-09-26</lastmod>

+     <changefreq>daily</changefreq>

+    </url>

+        

+    <url>

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

+     <lastmod>2016-09-26</lastmod>

+     <changefreq>daily</changefreq>

+    </url>

+        

+    <url>

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

+     <lastmod>2016-09-26</lastmod>

+     <changefreq>daily</changefreq>

+    </url>

+        

+    

+

 </urlset>

\ 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 = 'chart10275e5014cf' class = 'rChart morris'></div>

+<div id = 'chart16f2218d1abb' class = 'rChart morris'></div>

 <script type='text/javascript'>

     var chartParams = {

- "element": "chart10275e5014cf",

+ "element": "chart16f2218d1abb",

 "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": "chart10275e5014cf",

+"id": "chart16f2218d1abb",

 "labels": "cites" 

 },

       chartType = "Bar"

@@ -17,7 +17,7 @@

 [![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-1.5.14-blue.svg?style=flat)](https://github.com/GuangchuangYu/ggtree)

-[![total](https://img.shields.io/badge/downloads-13439/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![total](https://img.shields.io/badge/downloads-13544/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

 [![month](https://img.shields.io/badge/downloads-1122/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-166-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)

+[![Altmetric](https://img.shields.io/badge/Altmetric-167-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*.

@@ -10,5 +10,13 @@ pages:

 - Documentation: documentation.md

 - FAQ: faq.md

 - Featured Articles: featuredArticles.md

+- My Software:

+  - ChIPseeker: ../mysoftware/ChIPseeker.md

+  - clusterProfiler: ../mysoftware/clusterProfiler.md

+  - DOSE: ../mysoftware/DOSE.md

+  - ggtree: ../mysoftware/ggtree.md

+  - GOSemSim: ../mysoftware/GOSemSim.md

+  - ReactomePA: ../mysoftware/ReactomePA.md

+

 copyright: Copyright &copy; 2016 <a href="https://guangchuangyu.github.io">Guangchuang Yu</a>.<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div>

new file mode 100644

@@ -0,0 +1 @@

+<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/ChIPseeker" />

new file mode 100644

@@ -0,0 +1 @@

+<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/DOSE" />

new file mode 100644

@@ -0,0 +1 @@

+<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/GOSemSim" />

new file mode 100644

@@ -0,0 +1 @@

+<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/ReactomePA" />

new file mode 100644

@@ -0,0 +1 @@

+<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/clusterProfiler" />

new file mode 100644

@@ -0,0 +1 @@

+<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/ggtree" />

new file mode 100644

@@ -0,0 +1,216 @@

+<!DOCTYPE html>

+<html lang="en">

+    <head>

+        <meta charset="utf-8">

+        <meta http-equiv="X-UA-Compatible" content="IE=edge">

+        <meta name="viewport" content="width=device-width, initial-scale=1.0">

+        

+        <meta name="author" content="Guangchuang Yu">

+        <link rel="canonical" href="https://guangchuangyu.github.io/mysoftware/ChIPseeker/">

+        <link rel="shortcut icon" href="../../img/favicon.ico">

+

+	<title>ChIPseeker - ggtree</title>

+

+        <link href="../../css/bootstrap-custom.min.css" rel="stylesheet">

+        <link href="../../css/font-awesome-4.0.3.css" rel="stylesheet">

+        <link rel="stylesheet" href="../../css/highlight.css">

+        <link href="../../css/base.css" rel="stylesheet">

+

+        <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->

+        <!--[if lt IE 9]>

+            <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>

+            <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script>

+        <![endif]-->

+

+        

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+            m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)

+            })(window,document,'script','//www.google-analytics.com/analytics.js','ga');

+

+            ga('create', 'UA-77901140-1', 'guangchuangyu.github.io');

+            ga('send', 'pageview');

+        </script>

+        

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+

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+

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+            <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">

+                <span class="sr-only">Toggle navigation</span>

+                <span class="icon-bar"></span>

+                <span class="icon-bar"></span>

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+            </button>

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+        </div>

+

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+                </li>

+            

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+                <li >

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+                </li>

+            

+            

+            

+                <li class="dropdown active">

+                    <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a>

+                    <ul class="dropdown-menu">

+                    

+                        

+<li class="active">

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

+</li>

+

+                    

+                        

+<li >

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

+</li>

+

+                    

+                        

+<li >

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

+</li>

+

+                    

+                        

+<li >

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

+</li>

+

+                    

+                        

+<li >

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

+</li>

+

+                    

+                        

+<li >

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

+</li>

+

+                    

+                    </ul>

+                </li>

+            

+            

+            </ul>

+

+            <!-- Search, Navigation and Repo links -->

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

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+                            <i class="fa fa-github"></i>

+                        

+                        GitHub

+                    </a>

+                </li>

+                

+            </ul>

+        </div>

+    </div>

+</div>

+

+        <div class="container">

+            <div class="col-md-3"><div class="bs-sidebar hidden-print affix well" role="complementary">

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+        </div>

+

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+            <hr>

+            

+                <center>Copyright &copy; 2016 <a href="https://guangchuangyu.github.io">Guangchuang Yu</a>.<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div></center>

+            

+            <center>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</center>

+        </footer>

+

+        <script src="../../js/jquery-1.10.2.min.js"></script>

+        <script src="../../js/bootstrap-3.0.3.min.js"></script>

+        <script src="../../js/highlight.pack.js"></script>

+        <script>var base_url = '../..';</script>

+        <script data-main="../../mkdocs/js/search.js" src="../../mkdocs/js/require.js"></script>

+        <script src="../../js/base.js"></script>

+

+        <div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true">

+            <div class="modal-dialog">

+                <div class="modal-content">

+                    <div class="modal-header">

+                        <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">&times;</span><span class="sr-only">Close</span></button>

+                        <h4 class="modal-title" id="exampleModalLabel">Search</h4>

+                    </div>

+                    <div class="modal-body">

+                        <p>

+                            From here you can search these documents. Enter

+                            your search terms below.

+                        </p>

+                        <form role="form">

+                            <div class="form-group">

+                                <input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query">

+                            </div>

+                        </form>

+                        <div id="mkdocs-search-results"></div>

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+                </div>

+            </div>

+        </div>

+    </body>

+</html>

\ No newline at end of file

new file mode 100644

@@ -0,0 +1,216 @@

+<!DOCTYPE html>

+<html lang="en">

+    <head>

+        <meta charset="utf-8">

+        <meta http-equiv="X-UA-Compatible" content="IE=edge">

+        <meta name="viewport" content="width=device-width, initial-scale=1.0">

+        

+        <meta name="author" content="Guangchuang Yu">

+        <link rel="canonical" href="https://guangchuangyu.github.io/mysoftware/DOSE/">

+        <link rel="shortcut icon" href="../../img/favicon.ico">

+

+	<title>DOSE - ggtree</title>

+

+        <link href="../../css/bootstrap-custom.min.css" rel="stylesheet">

+        <link href="../../css/font-awesome-4.0.3.css" rel="stylesheet">

+        <link rel="stylesheet" href="../../css/highlight.css">

+        <link href="../../css/base.css" rel="stylesheet">

+

+        <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->

+        <!--[if lt IE 9]>

+            <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>

+            <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script>

+        <![endif]-->

+

+        

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+            m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)

+            })(window,document,'script','//www.google-analytics.com/analytics.js','ga');

+

+            ga('create', 'UA-77901140-1', 'guangchuangyu.github.io');

+            ga('send', 'pageview');

+        </script>

+        

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+

+    <body>

+

+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">

+    <div class="container">

+

+        <!-- Collapsed navigation -->

+        <div class="navbar-header">

+            <!-- Expander button -->

+            <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">

+                <span class="sr-only">Toggle navigation</span>

+                <span class="icon-bar"></span>

+                <span class="icon-bar"></span>

+                <span class="icon-bar"></span>

+            </button>

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+            <a class="navbar-brand" href="../..">ggtree</a>

+        </div>

+

+        <!-- Expanded navigation -->

+        <div class="navbar-collapse collapse">

+            <!-- Main navigation -->

+            <ul class="nav navbar-nav">

+            

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+                </li>

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+                </li>

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+                <li >

+                    <a href="../../faq/">FAQ</a>

+                </li>

+            

+            

+            

+                <li >

+                    <a href="../../featuredArticles/">Featured Articles</a>

+                </li>

+            

+            

+            

+                <li class="dropdown active">

+                    <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a>

+                    <ul class="dropdown-menu">

+                    

+                        

+<li >

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

+</li>

+

+                    

+                        

+<li >

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

+</li>

+

+                    

+                        

+<li class="active">

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

+</li>

+

+                    

+                        

+<li >

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

+</li>

+

+                    

+                        

+<li >

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

+</li>

+

+                    

+                        

+<li >

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

+</li>

+

+                    

+                    </ul>

+                </li>

+            

+            

+            </ul>

+

+            <!-- Search, Navigation and Repo links -->

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