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README.md
# ggtree: a phylogenetic tree viewer for different types of tree annotations <!--[![Build Status](https://travis-ci.org/GuangchuangYu/ggtree.svg?branch=master)](https://travis-ci.org/GuangchuangYu/ggtree) [![Build Status](https://ci.appveyor.com/api/projects/status/github/GuangchuangYu/ggtree?svg=true)](https://ci.appveyor.com/project/GuangchuangYu/ggtree/branch/master)--> [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](http://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](http://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![post](http://www.bioconductor.org/shields/posts/ggtree.svg)](https://support.bioconductor.org/t/ggtree/) [![commit](http://www.bioconductor.org/shields/commits/bioc/ggtree.svg)](http://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source) [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](http://bioconductor.org/packages/stats/bioc/ggtree.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 in the tree. ## Authors ## Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong. ## Citation ## Please cite the following article when using `ggtree`: ``` G Yu, D Smith, H Zhu, Y Guan, TTY Lam, ggtree: an R package for visualization and annotation of phylogenetic tree with different types of meta-data. Methods in Ecology and Evolution, submitted ``` ## License ## All source code is copyright, under the Artistic-2.0 License. For more information on Artistic-2.0 License see [http://opensource.org/licenses/Artistic-2.0](http://opensource.org/licenses/Artistic-2.0) ## Installation ## To install: * the latest released version: `biocLite("ggtree")` * the latest development version: `install_github("GuangchuangYu/ggtree")` ## Documentation ## + [viewing and annotating phylogenetic tree with ggtree](http://ygc.name/2014/12/21/ggtree/) + [updating a tree view using %<% operator](http://ygc.name/2015/02/10/ggtree-updating-a-tree-view/) + [an example of drawing beast tree using ggtree](http://ygc.name/2015/04/01/an-example-of-drawing-beast-tree-using-ggtree/) + [flip and rotate branches in ggtree](http://ygc.name/2015/07/01/flip-and-rotate-branches-in-ggtree/) + [ggtree with funny fonts](http://ygc.name/2015/06/12/ggtree-with-funny-fonts/) + [annotate phylogenetic tree with local images](http://ygc.name/2015/08/01/ggtree-annotate-phylogenetic-tree-with-local-images/) To view the vignette of `ggtree` installed in your system, start `R` and enter: ```r vignette("ggtree", package = "ggtree") ``` ## Bugs/Feature requests ## - If you have any, [let me know](https://github.com/GuangchuangYu/ggtree/issues). Thx!