deleted file mode 100644

@@ -1,112 +0,0 @@

-date: 2017-07-06T12:08:13+01:00

-title: 'ggtree: visualization and annotation of phylogenetic trees'

-type: index

-weight: 1

-

-

-

-<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">

-

-

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

-

-```{r echo=FALSE, results="hide", message=FALSE}

-library("ypages")

-```

-

-`r badge_bioc_release("ggtree", "blue")`

-`r badge_devel("guangchuangyu/ggtree", "blue")`

-`r badge_bioc_download("ggtree", "total", "blue")`

-`r badge_bioc_download("ggtree", "month", "blue")`

-

-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.

-*ggtree* is released within the [Bioconductor](https://bioconductor.org/packages/ggtree/) 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>.

-

-

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

-

-Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.

-

-

-## <i class="fa fa-book"></i> Citation

-

-Please cite the following article when using `ggtree`:

-

-

-`r badge_doi("10.1111/2041-210X.12628", "blue")`

-`r badge_altmetric("10533079", "blue")`

-`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "blue")`

-

-

-

-__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*__. 2017, 8(1):28-36.

-

-## <i class="fa fa-pencil"></i> Featured Articles

-

-![](https://guangchuangyu.github.io/featured_img/ggtree/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg)

-

-<i class="fa fa-hand-o-right"></i> Find out more on <i class="fa fa-pencil"></i> [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/).

-

-## <i class="fa fa-download"></i> Installation

-

-Install `ggtree` is easy, follow the guide on the [Bioconductor page](https://bioconductor.org/packages/ggtree/):

-

-```r

-## try http:// if https:// URLs are not supported

-source("https://bioconductor.org/biocLite.R")

-## biocLite("BiocUpgrade") ## you may need this

-biocLite("ggtree")

-```

-

-If you have problems when installing some of the dependent packages, please refer to the [ggtree-installation](https://github.com/GuangchuangYu/ggtree/wiki/ggtree-installation) wiki page.

-

-## <i class="fa fa-cogs"></i> Overview

-

-#### <i class="fa fa-angle-double-right"></i> Getting tree into R

-

-+ tree parsers: bring evolution evidences to be used/analyzed in `R`

-+ `merge_tree`: allows evolution evidences to be merged and compared

-+ `fortify` methods: convert tree objects into tidy data frame

-

-#### <i class="fa fa-angle-double-right"></i> Tree visualization & annotation

-

-+ parsing tree as a collection of nodes allows grammar of graphics to be supported

-+ `geom_tree`: extends `ggplot2` to support tree structure

-+ several layers and functions for tree annotation

-+ supports annotating phylogenetic trees with user's own data

-

-#### <i class="fa fa-angle-double-right"></i> Tree manipulation

-

-+ helper functions for tree manipulation, make it possible to explore the tree visually

-

-<i class="fa fa-hand-o-right"></i> Find out details and examples on <i class="fa fa-book"></i> [Documentation](https://guangchuangyu.github.io/ggtree/documentation/).

-

-

-

-

-## <i class="fa fa-code-fork"></i> Projects that depend on _ggtree_

-

-`r pkg_depend_info("ggtree", "CRAN")`

-

-`r pkg_depend_info("ggtree", "BioC")`

-

-

-#### <i class="fa fa-angle-double-right"></i> Other applications

-

-+ [BreadCrumbs](https://bitbucket.org/biobakery/breadcrumbs): Collection of scripts for metagenomics analysis

-+ [DegeneratePrimerTools](https://github.com/esnapd/DegeneratePrimerTools): Utilities for Creating and Validating Degenerate primers

-+ [phyloscan](https://github.com/olli0601/phyloscan): scan phylogenies created along a genome for patterns

-

-

-## <i class="fa fa-comments"></i> Feedback

-

-<ul class="fa-ul">

-<li><i class="fa-li fa fa-hand-o-right"></i> Please make sure you have followed <a href="https://guangchuangyu.github.io/2016/07/how-to-bug-author/"><strong>the important guide</strong></a> before posting any issue/question</li>

-<li><i class="fa-li fa fa-bug"></i> For bugs or feature requests, please post to <i class="fa fa-github-alt"></i> <a href="https://github.com/GuangchuangYu/ggtree/issues">github issue</a></li>

-<li><i class="fa-li fa fa-question"></i>  For user questions, please post to <i class="fa fa-google"></i> <a href="https://groups.google.com/forum/#!forum/bioc-ggtree">google group</a></li>

-<li><i class="fa-li fa fa-support"></i> We are also following every post tagged with <strong>ggtree</strong> on <a href="https://support.bioconductor.org">Bioconductor support site</a> and <a href="https://www.biostars.org">Biostars</a></li>

-<li><i class="fa-li fa fa-commenting"></i> 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>

@@ -1,5 +1,5 @@

 ---

-date: 2017-07-08T21:07:13+01:00

+date: 2017-07-06T12:08:13+01:00

 title: 'ggtree: visualization and annotation of phylogenetic trees'

 type: index

 weight: 1

@@ -7,15 +7,15 @@ weight: 1

-```{r echo=FALSE, results="hide", message=FALSE}

-library("ypages")

-```

+<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">

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

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

-<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">

+```{r echo=FALSE, results="hide", message=FALSE}

+library("ypages")

+```

 `r badge_bioc_release("ggtree", "blue")`

 `r badge_devel("guangchuangyu/ggtree", "blue")`

@@ -2,7 +2,7 @@

 date: 2017-07-08T21:07:13+01:00

 title: 'ggtree: visualization and annotation of phylogenetic trees'

 type: index

-weight: 0

+weight: 1

 ---

@@ -6,11 +6,6 @@ weight: 0

 ---

-# ggtree: visualization and annotation of phylogenetic trees

-

-

-`r ypages:::addtoany()`

-

 ```{r echo=FALSE, results="hide", message=FALSE}

 library("ypages")

@@ -35,13 +30,6 @@ The `ggtree` package extending the *ggplot2* package. It based on grammar of gra

 Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.

-<a href="https://twitter.com/guangchuangyu"><i class="fa fa-twitter fa-3x"></i></a>

-<a href="https://guangchuangyu.github.io/blog_images/biobabble.jpg"><i class="fa fa-wechat fa-3x"></i></a>

-<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Guangchuang+Yu[Author+-+Full]"><i class="ai ai-pubmed ai-3x"></i></a>

-<a href="https://scholar.google.com.hk/citations?user=DO5oG40AAAAJ&hl=en"><i class="ai ai-google-scholar ai-3x"></i></a>

-<a href="https://orcid.org/0000-0002-6485-8781"><i class="ai ai-orcid ai-3x"></i></a>

-<a href="https://impactstory.org/u/0000-0002-6485-8781"><i class="ai ai-impactstory ai-3x"></i></a>

-

 ## <i class="fa fa-book"></i> Citation

@@ -116,9 +104,9 @@ If you have problems when installing some of the dependent packages, please refe

 ## <i class="fa fa-comments"></i> Feedback

 <ul class="fa-ul">

-	<li><i class="fa-li fa fa-hand-o-right"></i> Please make sure you have followed <a href="https://guangchuangyu.github.io/2016/07/how-to-bug-author/"><strong>the important guide</strong></a> before posting any issue/question</li>

-	<li><i class="fa-li fa fa-bug"></i> For bugs or feature requests, please post to <i class="fa fa-github-alt"></i> <a href="https://github.com/GuangchuangYu/ggtree/issues">github issue</a></li>

-	<li><i class="fa-li fa fa-question"></i>  For user questions, please post to <i class="fa fa-google"></i> <a href="https://groups.google.com/forum/#!forum/bioc-ggtree">google group</a></li>

-	<li><i class="fa-li fa fa-support"></i> We are also following every post tagged with <strong>ggtree</strong> on <a href="https://support.bioconductor.org">Bioconductor support site</a> and <a href="https://www.biostars.org">Biostars</a></li>

-	<li><i class="fa-li fa fa-commenting"></i> 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>

+<li><i class="fa-li fa fa-hand-o-right"></i> Please make sure you have followed <a href="https://guangchuangyu.github.io/2016/07/how-to-bug-author/"><strong>the important guide</strong></a> before posting any issue/question</li>

+<li><i class="fa-li fa fa-bug"></i> For bugs or feature requests, please post to <i class="fa fa-github-alt"></i> <a href="https://github.com/GuangchuangYu/ggtree/issues">github issue</a></li>

+<li><i class="fa-li fa fa-question"></i>  For user questions, please post to <i class="fa fa-google"></i> <a href="https://groups.google.com/forum/#!forum/bioc-ggtree">google group</a></li>

+<li><i class="fa-li fa fa-support"></i> We are also following every post tagged with <strong>ggtree</strong> on <a href="https://support.bioconductor.org">Bioconductor support site</a> and <a href="https://www.biostars.org">Biostars</a></li>

+<li><i class="fa-li fa fa-commenting"></i> 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>

new file mode 100644

@@ -0,0 +1,124 @@

+---

+date: 2017-07-08T21:07:13+01:00

+title: 'ggtree: visualization and annotation of phylogenetic trees'

+type: index

+weight: 0

+---

+

+

+# ggtree: visualization and annotation of phylogenetic trees

+

+

+`r ypages:::addtoany()`

+

+

+```{r echo=FALSE, results="hide", message=FALSE}

+library("ypages")

+```

+

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

+

+

+<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">

+

+`r badge_bioc_release("ggtree", "blue")`

+`r badge_devel("guangchuangyu/ggtree", "blue")`

+`r badge_bioc_download("ggtree", "total", "blue")`

+`r badge_bioc_download("ggtree", "month", "blue")`

+

+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.

+*ggtree* is released within the [Bioconductor](https://bioconductor.org/packages/ggtree/) 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>.

+

+

+## <i class="fa fa-user"></i> Authors

+

+Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.

+

+<a href="https://twitter.com/guangchuangyu"><i class="fa fa-twitter fa-3x"></i></a>

+<a href="https://guangchuangyu.github.io/blog_images/biobabble.jpg"><i class="fa fa-wechat fa-3x"></i></a>

+<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Guangchuang+Yu[Author+-+Full]"><i class="ai ai-pubmed ai-3x"></i></a>

+<a href="https://scholar.google.com.hk/citations?user=DO5oG40AAAAJ&hl=en"><i class="ai ai-google-scholar ai-3x"></i></a>

+<a href="https://orcid.org/0000-0002-6485-8781"><i class="ai ai-orcid ai-3x"></i></a>

+<a href="https://impactstory.org/u/0000-0002-6485-8781"><i class="ai ai-impactstory ai-3x"></i></a>

+

+

+## <i class="fa fa-book"></i> Citation

+

+Please cite the following article when using `ggtree`:

+

+

+`r badge_doi("10.1111/2041-210X.12628", "blue")`

+`r badge_altmetric("10533079", "blue")`

+`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "blue")`

+

+

+

+__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*__. 2017, 8(1):28-36.

+

+## <i class="fa fa-pencil"></i> Featured Articles

+

+![](https://guangchuangyu.github.io/featured_img/ggtree/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg)

+

+<i class="fa fa-hand-o-right"></i> Find out more on <i class="fa fa-pencil"></i> [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/).

+

+## <i class="fa fa-download"></i> Installation

+

+Install `ggtree` is easy, follow the guide on the [Bioconductor page](https://bioconductor.org/packages/ggtree/):

+

+```r

+## try http:// if https:// URLs are not supported

+source("https://bioconductor.org/biocLite.R")

+## biocLite("BiocUpgrade") ## you may need this

+biocLite("ggtree")

+```

+

+If you have problems when installing some of the dependent packages, please refer to the [ggtree-installation](https://github.com/GuangchuangYu/ggtree/wiki/ggtree-installation) wiki page.

+

+## <i class="fa fa-cogs"></i> Overview

+

+#### <i class="fa fa-angle-double-right"></i> Getting tree into R

+

++ tree parsers: bring evolution evidences to be used/analyzed in `R`

++ `merge_tree`: allows evolution evidences to be merged and compared

++ `fortify` methods: convert tree objects into tidy data frame

+

+#### <i class="fa fa-angle-double-right"></i> Tree visualization & annotation

+

++ parsing tree as a collection of nodes allows grammar of graphics to be supported

++ `geom_tree`: extends `ggplot2` to support tree structure

++ several layers and functions for tree annotation

++ supports annotating phylogenetic trees with user's own data

+

+#### <i class="fa fa-angle-double-right"></i> Tree manipulation

+

++ helper functions for tree manipulation, make it possible to explore the tree visually

+

+<i class="fa fa-hand-o-right"></i> Find out details and examples on <i class="fa fa-book"></i> [Documentation](https://guangchuangyu.github.io/ggtree/documentation/).

+

+

+

+

+## <i class="fa fa-code-fork"></i> Projects that depend on _ggtree_

+

+`r pkg_depend_info("ggtree", "CRAN")`

+

+`r pkg_depend_info("ggtree", "BioC")`

+

+

+#### <i class="fa fa-angle-double-right"></i> Other applications

+

++ [BreadCrumbs](https://bitbucket.org/biobakery/breadcrumbs): Collection of scripts for metagenomics analysis

++ [DegeneratePrimerTools](https://github.com/esnapd/DegeneratePrimerTools): Utilities for Creating and Validating Degenerate primers

++ [phyloscan](https://github.com/olli0601/phyloscan): scan phylogenies created along a genome for patterns

+

+

+## <i class="fa fa-comments"></i> Feedback

+

+<ul class="fa-ul">

+	<li><i class="fa-li fa fa-hand-o-right"></i> Please make sure you have followed <a href="https://guangchuangyu.github.io/2016/07/how-to-bug-author/"><strong>the important guide</strong></a> before posting any issue/question</li>

+	<li><i class="fa-li fa fa-bug"></i> For bugs or feature requests, please post to <i class="fa fa-github-alt"></i> <a href="https://github.com/GuangchuangYu/ggtree/issues">github issue</a></li>

+	<li><i class="fa-li fa fa-question"></i>  For user questions, please post to <i class="fa fa-google"></i> <a href="https://groups.google.com/forum/#!forum/bioc-ggtree">google group</a></li>

+	<li><i class="fa-li fa fa-support"></i> We are also following every post tagged with <strong>ggtree</strong> on <a href="https://support.bioconductor.org">Bioconductor support site</a> and <a href="https://www.biostars.org">Biostars</a></li>

+	<li><i class="fa-li fa fa-commenting"></i> 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>