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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.

This page is an annotated directory of documentation, software, and other products related to the project.

General

• 'About' page - general information about the project, with a list of personnel and further links.
• Contact page - with links to mailing lists and IRC
• "Synthesis of phylogeny and taxonomy into a comprehensive tree of life" - PNAS article describing the project.
• Project blog
• First grant proposal
• Trello board for software development - probably quite rusty

Web applications

We have web applications for browsing the synthetic tree, browsing the Open Tree Taxonomy (OTT), and a curation application for browsing the phylesystem and imputting published phylogenies.

• Phylesystem browser and curation tool
  • Instructions for submitting phylogenetic trees
• Synthetic tree browser
  • See PNAS article for how we made the tree
• Reference taxonomy (OTT) browser
  • Description of the reference taxonomy

Documentation for programmers using the phylesystem and Open Tree services

• Web API v2
  • Web API v2 documentation - the web API enables access to the corpus, and provides other services
  • Tutorials - how to do things with the APIs
• Libraries (service bindings and wrappers, etc.)
  • The peyotl phylesystem management library - you can use it with the APIs or 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
• Web API v3
  • Web API v3 documentation
• Static files
  • Supertree downloads
  • Taxonomy downloads
  • Version 3 (v3) Open Tree of Life Web APIs - in preparation, not yet 'released'

System internals

• Repository list - a more complete list of the repositories with a brief description of each
• Phylesystem management
  • Bioinformatics publication on phylesystem
  • peyotl - library for phylesystem access and update
    • peyotl documentation
  • phylesystem-api - Web API for access
  • oti - phylesystem indexing
  • Nexson file format - 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.
  • NeXML - XML document format on which Nexson is based.
  • Document store requirements gathering prepared in advance of implementing the phylesystem
• opentree - web application for tree curation and supertree browsing
  • Phylografter (tree curation) user interviews
• Supertree construction methods
  • treemachine - used to create the synthetic trees up to draftversion4
  • propinquity - new method under development
  • Propinquity documentation: inputs, outputs, how to run
  • Propinquity synthetic tree annotations and conflict relations
  • Phylogenetic graph for finding a supertree based on ranks
• Reference taxonomy
  • reference-taxonomy - taxonomy construction ("smasher")
  • reference-taxonomy wiki - taxonomy documentation
  • taxomachine - taxonomic name resolver (TNRS)
  • Taxonomy downloads
• ArguSON
• System integration
  • germinator - the germinator repository and its wiki hold code, tests, and documentation that relate subsystems to one another, or that otherwise don't belong to any single subsystem
  • Web API testing
  • Service deployment system
  • Caching results from common API calls