Description
Discovery, Access and Manipulation of 'TreeBASE' Phylogenies.
Description
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.
README.md
treebase
An R package for discovery, access and manipulation of online phylogenies
- [Publication in Methods in Ecology and Evolution doi:10.1111/j.2041-210X.2012.00247.x
Installation
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.
library(devtools)
install_github("ropensci/treebase")
Getting Started
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.
- treebase is part of the rOpenSci Project
References
- 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.