Interface to the API for 'TreeBASE' < http://treebase.org> from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic trees (of species, population, or genes) and the data used to create them.
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.
Use of the
treebase package should be relatively straight forward:
library(treebase)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