The book gives comprehensive overviews of phylogenetic tree data integration, manipulation and visualization using a suite of R packages, tidytree, treeio and ggtree. The book is available at https://yulab-smu.github.io/treedata-book/.

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

1. 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.
2. 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.