ggtree: visualization and annotation of phylogenetic trees
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
Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.
Please cite the following article when using
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.
ggtree is easy, follow the guide on the Bioconductor
## 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.
Getting tree into R
- tree parsers: bring evolution evidences to be used/analyzed in
merge_tree: allows evolution evidences to be merged and compared
fortifymethods: convert tree objects into tidy data frame
Tree visualization & annotation
- parsing tree as a collection of nodes allows grammar of graphics to be supported
ggplot2to support tree structure
- several layers and functions for tree annotation
- supports annotating phylogenetic trees with user's own data
- helper functions for tree manipulation, make it possible to explore the tree visually
Find out details and examples on Documentation.
Projects that depend on ggtree
- harrietr: Wrangle Phylogenetic Distance Matrices and Other Utilities
- LINC: co-expression of lincRNAs and protein-coding genes
- philr: Phylogenetic partitioning based ILR transform for metagenomics data
- BreadCrumbs: Collection of scripts for metagenomics analysis
- DegeneratePrimerTools: Utilities for Creating and Validating Degenerate primers
- phyloscan: scan phylogenies created along a genome for patterns
- Please make sure you have followed the important guide before posting any issue/question
- For bugs or feature requests, please post to github issue
- For user questions, please post to google group
- We are also following every post tagged with ggtree on Bioconductor support site and Biostars
- Join the group chat on and