ggtree: tree visualization and annotation

knitr::opts_chunk$set(tidy = FALSE,
           message = FALSE)
CRANpkg <- function (pkg) {
    cran <- ""
    fmt <- "[%s](%s=%s)"
    sprintf(fmt, pkg, cran, pkg)

Biocpkg <- function (pkg) {
    sprintf("[%s](", pkg, pkg)


Please go to for the full vignette.


If you use r Biocpkg('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.
  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.

Need helps?

If you have questions/issues, please visit ggtree homepage first. Your problems are mostly documented.

If you think you found a bug, please follow the guide and provide a reproducible example to be posted on github issue tracker. For questions, please post to google group. Users are highly recommended to subscribe to the mailing list.

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ggtree documentation built on Nov. 15, 2020, 2:09 a.m.