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<!-- is generated from README.Rmd. Please edit that file --> # treeio: Base classes and functions for phylogenetic tree input and output <a href=""><img src="man/figures/logo.png" align="right" height="139" /></a> [![](]( [![Bioc](]( [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](]( [![platform](]( [![codecov](]( [![](]( [![](]( [![Linux Travis Build Status](]( [![AppVeyor Build Status](]( [![](]( [![](]( [![download](]( ‘treeio’ is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats. Visit <> for details. [![Twitter](]( [![saythanks](]( [![](]( ## :writing_hand: Authors Guangchuang YU School of Basic Medical Sciences, Southern Medical University <> If you use [treeio]( in published research, please cite: - 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**<sup>\*</sup>. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. ***Molecular Biology and Evolution***. 2020, 37(2):599-603. doi: [10.1093/molbev/msz240]( ## :arrow_double_down: Installation Get the released version from Bioconductor: ``` r ## try http:// if https:// URLs are not supported if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") ## BiocManager::install("BiocUpgrade") ## you may need this BiocManager::install("treeio") ``` Or the development version from github: ``` r ## install.packages("devtools") devtools::install_github("YuLab-SMU/treeio") ``` ## :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]( ## :houses: Package Affiliations The `treeio` package is a part of the Bioconductor and rOpenSci projects. | [![bioconductor_footer](]( | [![ropensci_footer](]( | |:-------------------------------------------------------------------------------------------------------:|:----------------------------------------------------------------------------------------------:|