Preface

You can’t even begin to understand biology, you can’t understand life, unless you understand what it’s all there for, how it arose - and that means evolution.

— Richard Dawkins

The book is meant as a guide for data integration, manipulation and visualization of phylogenetic trees using a suite of R packages, tidytree, treeio and ggtree.

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

  1. LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu*. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution. 2019, accepted. doi: 10.1093/molbev/msz240.
  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.
  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.

The book’s source code is hosted on GitHub, at https://github.com/YuLab-SMU/treedata-book. If you notice typos or other issues, feel free to open an issue on GitHub or send me a pull request. If you do the latter, in your commit message, please add the sentence “I assign the copyright of this contribution to Guangchuang Yu,” so that I can maintain the option of publishing this book in other forms.

This work is licensed under the Attribution-NonCommercial-NoDerivatives 4.0 International License.