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Open Tree of Life: Start here

The goal of the Open Tree of Life project is to summarize and synthesize what is known about the phylogenetic relationships of life on Earth. The input data for the project centers around a corpus of phylogenetic trees, called the 'phylesystem'. All trees are aligned to a common reference taxonomy (called OTT for the Open Tree Taxonomy). The comprehensive 'synthetic tree' covering all life is created by merging OTT and a well-curated subset of the trees in phylesystem.

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
• Project Roadmap

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
  • Web API v3 documentation
  • Web API v2 documentation
• 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
• Tutorials - how to do things with the APIs
• Static files
  • Supertree downloads
  • Taxonomy downloads
  • Version 3 (v3) Open Tree of Life Web APIs - in preparation, not yet 'released'
• Phylesystem API
  • Phylesystem v1 API - not updated to v3 yet, but contains detailed information not found in the main API documentation

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
  • propinquity - tool for making supertrees
  • [Propinquity documentation: inputs, outputs, how to run](https://github.com/OpenTreeOfLife/propinquity /blob/master/README.md)
  • Propinquity synthetic tree annotations and conflict relations
  • Phylogenetic graph for finding a supertree based on ranks
  • treemachine - used to create the synthetic trees up to draftversion4
• 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
• Building and deploying a new synthetic tree
• Deploying a new taxonomy version

Supertree method

• Summarizing a taxonomy and multiple estimates of phylogenetic trees
• Pipeline diagram

Old/deprecated resources

• Trello board for software development - probably quite rusty