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2nexml

command tool for creating NeXML from other file formats

amendments-0

Test data for taxonomic amendments API (peyotl)

amendments-1

Production data for taxonomic amendments API (peyotl)

argus

tree/graph viewer and conflict visualizer for the opentree project

assesssupertrees

Used to assess the supertree using RF distance, quartet distance, support and conflict (following Mark Wilkinson et al 2006) etc..

asterales-phylesystem

A phylesystem containing only studies that overlap Asterales.

big-tree-collection-simulator

simulator of collections of trees that are based on a classification with stochastic errors introduced

chronosynth

Match dates from chronograms in phylesystem to synthetic tree nodes

clade-workshops

OpenTree / FuturePhy workshops

collections-0

Collections of trees from the OpenTree datastore.

collections-1

Tree collections

deployed-systems

A collection of current (and past) server configuration files for opentree components

edotts

JSON edits usable as inputs to otc-taxonomy-patcher tool for editing OTT

eertgif

experimental project. yet another pdf2newick converter

favorites-0

User-specific items of interest (clades, collections, other users) in Open Tree

feedback

No code -- just an issue tracker for general feedback (sent here via GitHub's issues API)

files.opentreeoflife.org

Static content related to the project; the webroot for the files.opentreeoflife.org web site. The repo contains all of the smallish files: indexes, READMEs, and so on. Larger files such as taxonomies and synthetic trees on the web site but not in git.

gcmdr

Graph of Life Commander

germinator

miscellaneous scripts and data for concerns that span more than one of the Open Tree code repositories: integration tests, system statistics, etc.

git_wrap_opentree

hackathon

A repo for the 2014 OpenTree / Arbor / HIP hackathon

hbf_phylesystem_test

temp repo for testing api when nexsons are stored in 1.2.1 syntax

illustrations-0

Test data repository for Tree Illustrator

muriqui

An annotation database for decorating nodes in trees

ncl

Nexus Class Library

nexson

python parsing of Open Tree of Life's NexSON format. Formerly a part of the peyotl package

nexson-sandbox

Initially a collection of nexson files to test parsing; might also be useful for testing repository implementations

opentree

Opentree browsing and curation web site. For overarching or cross-repo concerns, please see the 'germinator' repo.

opentree-install

A demo installation of open tree of life using ansible playbooks.

opentree-testrunner

Scripts for testing some of the software tools produced by the Open Tree of Life effort