@@ -52,7 +52,11 @@ site:

 	cd ..

 preview:

-	Rscript -e 'setwd("site_src"); blogdown::serve_site()'

+	cd site_src;\

+	ln -s ../../software/themes themes;\

+	Rscript -e 'blogdown::serve_site()';\

+	rm themes;\

+	cd ..

 mkdocs: mdfiles

 	cd mkdocs;\

@@ -344,6 +344,12 @@

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

 <div class="figure">

+<img src="http://media.springernature.com/lw785/springer-static/image/art%3A10.1186%2Fs40168-017-0331-1/MediaObjects/40168_2017_331_Fig3_HTML.gif" />

+

+</div>

+<p><a href="https://doi.org/10.1186/s40168-017-0331-1" class="uri">https://doi.org/10.1186/s40168-017-0331-1</a></p>

+<hr />

+<div class="figure">

 <img src="https://guangchuangyu.github.io/featured_img/ggtree/syen12249-fig-0002.png" />

 </div>

@@ -18,7 +18,8 @@

       <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>

       <guid>https://guangchuangyu.github.io/ggtree/gallery/</guid>

-      <description>https://doi.org/10.1111/syen.12249

+      <description>https://doi.org/10.1186/s40168-017-0331-1

+ https://doi.org/10.1111/syen.12249

  https://doi.org/10.1186/s12915-017-0402-6

  http://dx.doi.org/10.3389/fmicb.2017.00543

  https://doi.org/10.3389/fmicb.2017.00456

@@ -345,7 +345,7 @@

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

 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>

-<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.2-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.4-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-18565/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-834/month-blue.svg?style=flat" alt="month" /></a></p>

+<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.2-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.4-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-18823/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-941/month-blue.svg?style=flat" alt="month" /></a></p>

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

 <div id="authors" class="section level2">

 <h2><i class="fa fa-user"></i> Authors</h2>

@@ -354,7 +354,7 @@

 <div id="citation" class="section level2">

 <h2><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 src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-345-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-36-blue.svg?style=flat" alt="citation" /></a></p>

+<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-345-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-39-blue.svg?style=flat" alt="citation" /></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>. 2017, 8(1):28-36.</p>

 </div>

 <div id="featured-articles" class="section level2">

@@ -60,7 +60,8 @@ Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotid

       <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>

       <guid>https://guangchuangyu.github.io/ggtree/gallery/</guid>

-      <description>https://doi.org/10.1111/syen.12249

+      <description>https://doi.org/10.1186/s40168-017-0331-1

+ https://doi.org/10.1111/syen.12249

  https://doi.org/10.1186/s12915-017-0402-6

  http://dx.doi.org/10.3389/fmicb.2017.00543

  https://doi.org/10.3389/fmicb.2017.00456

@@ -8,6 +8,12 @@ weight: 40

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

 <div class="figure">

+<img src="http://media.springernature.com/lw785/springer-static/image/art%3A10.1186%2Fs40168-017-0331-1/MediaObjects/40168_2017_331_Fig3_HTML.gif" />

+

+</div>

+<p><a href="https://doi.org/10.1186/s40168-017-0331-1" class="uri">https://doi.org/10.1186/s40168-017-0331-1</a></p>

+<hr />

+<div class="figure">

 <img src="https://guangchuangyu.github.io/featured_img/ggtree/syen12249-fig-0002.png" />

 </div>

@@ -9,7 +9,7 @@ weight: 1

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

 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>

-<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.2-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.4-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-18565/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-834/month-blue.svg?style=flat" alt="month" /></a></p>

+<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.2-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.4-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-18823/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-941/month-blue.svg?style=flat" alt="month" /></a></p>

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

 <div id="authors" class="section level2">

 <h2><i class="fa fa-user"></i> Authors</h2>

@@ -18,7 +18,7 @@ weight: 1

 <div id="citation" class="section level2">

 <h2><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 src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-345-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-36-blue.svg?style=flat" alt="citation" /></a></p>

+<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-345-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-39-blue.svg?style=flat" alt="citation" /></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>. 2017, 8(1):28-36.</p>

 </div>

 <div id="featured-articles" class="section level2">