Discovery, Access and Manipulation of 'TreeBASE' Phylogenies

Interface to the API for 'TreeBASE' <> from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic trees (of species, population, or genes) and the data used to create them.

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An R package for discovery, access and manipulation of online phylogenies


treebase is available from CRAN. You can install the latest version from the development website on github using the devtools package from within R. Make sure you have the latest version for the best experience.


Getting Started

Use of the treebase package should be relatively straight forward:

Phylogenies_from_Huelsenbeck <- search_treebase("Huelsenbeck", "author")

More interesting examples will take advantage of R to loop over large amounts of treebase data that would be to tiresome to search for, download and analyze by hand. Welcome to the era of big data phylogenetics.

  • Browse the examples in the documentation

  • We are preparing a short manuscript to introduce the motivation, functions, and use-cases for the treebase package. Meanwhile, a preprint is available as a dynamic document, where all of the examples shown are produced by the code shown using knitr. See source code.

  • treebase is part of the rOpenSci Project


  • Carl Boettiger, Duncan Temple Lang (2012). Treebase: An R package for discovery, access and manipulation of online phylogenies, Methods in Ecology and Evolution. doi:10.1111/j.2041-210X.2012.00247.x


version 0.1.4

  • Drop laser dependency since laser is deprecated

version 0.1.3

  • Declare VignetteBuilder

version 0.1.2


  • bugfix for performance issues on downloading trees

version 0.1.1

  • Make tests run on CRAN faster and more robust

version 0.1.0

  • update unit test structure for newer testthat version
  • switch to semantic version numbering

version 0.0-7.1

version 0.0-7

  • exclude unnecessary files

version 0.0-5

  • Improved error handling
  • Will allow multiple attempts if fails to access resource
  • Search now supports query by doi
  • updated caches
  • outdated demos removed

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.


0.1.4 by Carl Boettiger, 5 years ago

Report a bug at

Browse source code at

Authors: Carl Boettiger [aut, cre] , Duncan Temple Lang [aut]

Documentation:   PDF Manual  

Task views: Phylogenetics, Especially Comparative Methods

CC0 license

Imports XML, RCurl, methods, utils, httr

Depends on ape

Suggests testthat, knitr, rmarkdown

Imported by datelife.

See at CRAN