---
date: 2017-07-06T12:08:13+01:00
title: 'ggtree: visualization and annotation of phylogenetic trees'
type: index
weight: 1
---
```{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 GitHub.
## 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`:
`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\*. 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.
## Featured Articles
Find out more on [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/).
## 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.
## Overview
#### 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
#### 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
#### Tree manipulation
+ helper functions for tree manipulation, make it possible to explore the tree visually
Find out details and examples on [Documentation](https://guangchuangyu.github.io/ggtree/documentation/).
## Projects that depend on _ggtree_
`r pkg_depend_info("ggtree", "CRAN")`
`r pkg_depend_info("ggtree", "BioC")`
#### 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
## Feedback
Please make sure you have followed the important guide before posting any issue/question
For bugs or feature requests, please post to github issue
```{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 GitHub.
## 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`:
`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\*. 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.
## Featured Articles
Find out more on [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/).
## 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.
## Overview
#### 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
#### 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
#### Tree manipulation
+ helper functions for tree manipulation, make it possible to explore the tree visually
Find out details and examples on [Documentation](https://guangchuangyu.github.io/ggtree/documentation/).
## Projects that depend on _ggtree_
`r pkg_depend_info("ggtree", "CRAN")`
`r pkg_depend_info("ggtree", "BioC")`
#### 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
## Feedback