‘ggtree’ extends the ‘ggplot2’ plotting system which implemented the grammar of graphics. ‘ggtree’ is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.

For details, please visit https://yulab-smu.top/treedata-book/.

Guangchuang YU

School of Basic Medical Sciences, Southern Medical University

https://guangchuangyu.github.io

If you use ggtree in published research, please cite the most appropriate paper(s) from this list:

1. G Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96.
   • Source code and data to reproduce figures in the article
2. G Yu^*, TTY Lam, H Zhu, Y Guan^*. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. doi: 10.1093/molbev/msy194.
   • Source code to produce Supplementary Material
3. 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. doi: 10.1111/2041-210X.12628.

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