ggtree: visualization and annotation of phylogenetic trees

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 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:

citation

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.

Find out more on Featured Articles.

Installation

Install ggtree is easy, follow the guide on the Bioconductor page:

## 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 wiki page.

Overview

Getting tree into R

Tree visualization & annotation

Tree manipulation

Find out details and examples on Documentation.

Projects that depend on ggtree

CRAN packages

Bioconductor packages

Other applications

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