treeio: Base classes and functions for parsing and exporting phylogenetic tree

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The treeio package defines classes and functions for parsing and exporting phylogenetic trees. treeio is released within the Bioconductor project and the source code is hosted on GitHub.

Authors

Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.

Citation

treeio was splitted from ggtree package, please cite the following article when using treeio:

doi Altmetric citation

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.

Installation

Install treeio is easy, follow the guide on the Bioconductor page:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
## biocLite("BiocUpgrade") ## you may need this
biocLite("treeio")

Overview

Supported tree format:

  • Newick
  • NEXUS
  • New Hampshire eXtended format (NHX)
  • Jplace
  • Phylip

Supported software output:

  • BEAST
  • EPA
  • HYPHY
  • MrBayes
  • PHYLODOG
  • phyloT
  • pplacer
  • r8s
  • RAxML
  • RevBayes

Tree manipulation

  • merge_tree for merging evolutionary evidences inferred from different phylogenetic analyses

Find out details and examples on Documentation.

Projects that depend on treeio

Bioconductor packages

  • ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

Feedback

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