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Open Tree of Life: Start here

The Open Tree of Life project centers around a corpus of phylogenetic trees, called the 'phylesystem'. All trees are aligned to a common reference taxonomy (OTT). One application of the phylesystem is to provide the inputs for creating a 'supertree' covering all life.

Some general information about the project, with a list of personnel, is here.

The web applications

Corpus browser and study curation tool

Start the phylesystem browser and curation tool here. If you are submitting trees, you are encouraged to read the tree submission documentation first.

Supertree browser

Start the supertree browser web application here. For a description of how the supertree was made, see the article "Synthesis of phylogeny and taxonomy into a comprehensive tree of life".

Reference taxonomy browser

Browse the reference taxonomy here. For description of the taxonomy see here.

Documentation for programmers using the phylesystem and Open Tree services

There is a web API that enables access to the corpus, and provides other services.

V2 API documentation
Tutorials - how to do things with the APIs

There are also some libraries for working with opentree in various languages (service bindings and wrappers, etc.)

The peyotl phylesystem management library - you can use it with your own local clone of phylesystem
rotl - an R package that wraps the OpenTree APIs
Other libraries - packages in R, python, and Ruby developed at a 2014 hackathon

Software overview

The software is divided into subsystems, each of which has its own github repository.

The main software functions are:

corpus management (peyotl repo), access (phylesystem-api repo), and indexing (oti repo) (see article)
user-facing web application for tree curation (opentree repo)
supertree methods (treemachine repo, propinquity repo) for making an all-life supertree
reference taxonomy construction (reference-taxonomy repo) and taxonomic name resolver (taxomachine repo)

The germinator repository and its wiki hold code, tests, and documentation that relate subsystems to one another, or otherwise don't belong to any particular subsystem.

For a list of the repositories with a brief description of each, see here.

Some of the system-wide documentation of the kind that properly belongs in the germinator repository is currently housed in the opentree repository wiki, for historical reasons. Many of these documents cover topics far beyond the web app. It is intended that these documents will move to the germinator repository eventually.

Nexson

Each tree belongs to a published study, so trees belonging to a study are collected together into a 'Nexson file' for the study. The Nexson format is central to the architecture. It's derived from NeXML and is documented here.