CD2H gitForager

Login: OpenTreeOfLife

Company: null

Location: null

email:

Blog: http://opentreeoflife.github.io/

Members

Repositories

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
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
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.
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-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.
opentreeoflife.github.io: Organization page with description of repositories:
opentree-testrunner: Scripts for testing some of the software tools produced by the Open Tree of Life effort
ot-ansible: null
ot-base: General Java classes for Open Tree of Life development with Neo4j
otcetera: C++14 lib for parsing of trees from newick, nexson, and taxonomy.tsv formats; tree calculations and manipulations
otcmdr: Pipeline for building synthetic trees from Open Tree data
oti: indexing service for the OpenTreeOfLife nexson repository
otindex: opentree index using postgres and pyramid
otindex_ansible: ansible playbook for installation of OpenTree otindex
peyotl: python library for interacting with Open Tree of Life resources
phylesystem: phylogenetic study document storage used by Open Tree of Life
phylesystem-0: Yet another testing repository. This one is full size for performance testing. But still temporary.
phylesystem-1: doc store for the Open Tree of Life study curation API
phylesystem-api: API access to Open Tree of Life treestore
phylesystem_test: Testing repo which is a small subset of phylesystem
phylografter: web2py app for tree store and grafting
PhylografterNeo4j: null
propinquity: make-based supertree pipeline
pta: phylogeny-taxonomy alignment service
pyopentree: Python bindings for OpenTree services
reference-taxonomy: Open Tree Reference Taxonomy (OTT) tools
script-managed-trees: null
shared-api-tests: json-formatted specifications for unit testing frameworks
taxomachine: taxonomy graphdb
taxonomy-stree-json: JSON files for visualizing source trees aligned to taxonomies
tree-illustrator: Generate repeatable, data-driven, publication quality figures of trees.
treemachine: Source tree graph database
treeviz-workshop-2017: Workshop/hackathon for interoperability across tree viewers
ws_wrapper: OpenTree Web-Services Wrapper

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.