Using Open Tree of Life web-services

Workshops and Materials

Most up to date tutorials

R tutorials

See Luna Luisa Sanchez-Reyes’ Open Tree with R tutorial for a very nice introduction of how to efficiently use the rotl package and DateLife for interacting with Open Tree’s web services.

Python and Jupyter tutorials

Install instructions Getting a tree of all bird families Getting a tree for GBIF records Dating synthetic trees

Looking for conflicting phylogenetic claims

Our tree curation tool has a conflict viewer that allows you to compare a tree to the Open Tree Taxonomy or the Open Tree Synthetic tree. We are in the process of generalizing this feature so that biologists can compare any tree to any other tree. These trees will need to be mapped to the Open Tree Taxonomy.

API Docs

Our current API is documented at here

Older materials

Previous workshops

SSB 2020
Berkeley Feb 2020

Integrating Open Tree and GBIF

Emily Jane McTavish wrote a tutorial here covering some ways to use trees from Open Tree with geographic range data from GBIF.