Open Tree Reference Taxonomy (OTT) tools
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README.md

This is the repository for the Open Tree of Life reference taxonomy (OTT), which is only one part of the Open Tree of Life project.

For general Open Tree of Life project documentation see the germinator repository's wiki.

This repository contains the following:

  1. Smasher, a taxonomy manipulation tool
    • Java package taxa, general classes for taxa and taxonomies
    • Java package smasher, for combining taxonomies
    • Java package conflict, for conflict analysis
    • a variety of python utilities
  2. Scripts for creating the Open Tree reference taxonomy (OTT)
    • python and shell scripts for creating OTT
    • taxonomic source information, such as the separation taxonomy, Hibbett 2007, and Schaferhoff 2012
    • scripts for making the master OTT id list

How to use 'smasher'

See file doc/scripting.md for documentation on using the scripting features of smasher for building, subsetting, querying, and other operations on taxonomies.

Taxonomies are represented as directories, see here.

To test to see whether you can run Smasher successfully, do 'make test'.

If you're puzzled by some decision the algorithm has made, it can be helpful to look at output files log.tsv, choices.tsv, and conflicts.tsv.

How to create a new version of OTT

See the maintenance manual