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<!-- is generated from README.Rmd. Please edit that file --> # ggtree: an R package for visualization of phylogenetic trees with their annotation data <a href=""><img src="" height="200" align="right" /></a> [![platform](]( [![](]( [![codecov](]( [![Awesome](]( <!-- [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](]( [![Bioc](]( [![Last-changedate](]( ` r badge_devel("guangchuangyu/ggtree", "green")` ` r badge_bioc_download("ggtree", "total", "blue")` ` r badge_bioc_download("ggtree", "month", "blue")` ` r badge_bioc_download_rank("ggtree")` --> ‘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. ## :writing_hand: Authors Guangchuang YU School of Basic Medical Sciences, Southern Medical University <> [![Twitter](]( [![saythanks](]( [![](]( If you use [ggtree]( in published research, please cite the most appropriate paper(s) from this list: 1. S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan, **G Yu**. Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data. ***iMeta***, 2022, 1(4):e56. doi: [10.1002/imt2.56]( 2. **G Yu**. Data Integration, Manipulation and Visualization of Phylogenetic Treess (1st edition). ***Chapman and Hall/CRC***, 2022. doi: [10.1201/9781003279242]( 3. **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]( 4. **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. 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]( 5. **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. 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]( <center> <a href=""><img src="" style="width:500px;border:2px solid black;"/></a> </center> ## :sparkling_heart: Contributing We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the [Contributor Code of Conduct](