Overview

If you are looking for the git repo URL, it is: https://github.com/OpenTreeOfLife/peyotl

peyotl is a python package written to make it easier to interact with the software produced by the Open Tree of Life project. Specifically, to:

  1. interact with a local version of the phylesystem repository of curated phylogenetic studies ;

  2. call web services associated with the studies (served by web app running the phylesystem-api code);

  3. call web services associated with taxonomic resolution services (running taxomachine );

  4. call web services associated with Open Tree of Life’s “synthetic” estimate of the tree of life (running treemachine);

  5. call web services associated with an annotation database (that we have not built yet)

Currently peyotl is used to implement most of the functionality in the phylesystem-api backend of the study curation tool.

Documentation Table of Contents

  1. Installation
  2. Configuration
  3. Tutorials
  4. Testing
  5. Format conversion
  6. NexSON validation
  7. Phylesystem
  8. API wrappers
  9. Roadmap

Thanks

peyotl is primarily written by Mark Holder, Emily Jane McTavish, and Jim Allman, but see the contributors file for a more complete list of people who have contributed code.

The fabulous Karl Gude created the logo.

Several parts of the setup.py, logging, documentation, and test suite were based on Jeet Sukumraran’s work in the DendroPy package.

The sortattr.xslt stylesheet (which is only used in round-trip testing) is from http://stackoverflow.com/questions/1429991/using-xsl-to-sort-attributes

The peyotl.phylesystem.git_actions (and the tests) were a part of the api.opentreeoflife.org repo which was primarily the work of Duke Leto (at that time).

Jim Allman, Karen Cranston, Cody Hinchliff, Mark Holder, Peter Midford, and Jonathon Rees all participated in the discussions that led to the NexSON mapping.

The peyotl/test/data/nexson/phenoscape/nexml test file is from a Phenoscape file downloaded on Feb 16, 2014. The citation for the data is in the nexml doc itself.

Etymology: According to Wikipedia, peyotl is the Nahuatl word for Lophophora williamsii.