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    64 repositories

    • collections-1

      Public
      Tree collections
      Other
      •2•1•0•0•Updated Sep 16, 2025Sep 16, 2025

    • phylesystem-1

      Public
      doc store for the Open Tree of Life study curation API
      1•1•12•0•Updated Sep 16, 2025Sep 16, 2025

    • amendments-1

      Public
      Production data for taxonomic amendments API (peyotl)
      Other
      •2•2•0•0•Updated Aug 26, 2025Aug 26, 2025

    • nexson

      Public
      python parsing of Open Tree of Life's NexSON format. Formerly a part of the peyotl package
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Aug 22, 2025Aug 22, 2025

    • peyotl

      Public
      python library for interacting with Open Tree of Life resources
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •7•11•29•0•Updated Aug 22, 2025Aug 22, 2025

    • ot-ansible

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•8•0•Updated Aug 22, 2025Aug 22, 2025

    • webapp-tree-viewer

      Public
      Opentree synthetic-tree browser (standalone, in Pyramid)
      JavaScript
      •
      BSD 2-Clause "Simplified" License
      •26•1•0•0•Updated Aug 13, 2025Aug 13, 2025

    • opentree

      Public
      Opentree browsing and curation web site. For overarching or cross-repo concerns, please see the 'germinator' repo.
      JavaScript
      •
      BSD 2-Clause "Simplified" License
      •26•120•294•9•Updated Aug 11, 2025Aug 11, 2025

    • authomatic

      Public
      Modified to work with Python3.12 and Pyramid (OAuth2 problems)
      Python
      •
      MIT License
      •389•0•0•0•Updated Aug 6, 2025Aug 6, 2025

    • opentreeoflife.github.io

      Public
      Organization page with description of repositories:
      HTML
      •
      BSD 2-Clause "Simplified" License
      •1•10•0•0•Updated Jul 29, 2025Jul 29, 2025

    • peyutil

      Public
      Simple "utility" functions for Open Tree of Life's python code. Formerly part of the peyotl package
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Jun 26, 2025Jun 26, 2025

    • propinquity

      Public
      make-based supertree pipeline
      Python
      •
      BSD 2-Clause "Simplified" License
      •3•8•21•0•Updated Jun 24, 2025Jun 24, 2025

    • reference-taxonomy

      Public
      Open Tree Reference Taxonomy (OTT) tools
      Python
      •
      BSD 2-Clause "Simplified" License
      •12•10•137•0•Updated Jun 22, 2025Jun 22, 2025

    • edOTTs

      Public
      JSON edits usable as inputs to otc-taxonomy-patcher tool for editing OTT
      0•0•0•0•Updated Jun 20, 2025Jun 20, 2025

    • python-opentree

      Public
      Python package for working with Open Tree of Life webservices and artifacts. Importable as opentree
      Python
      •
      BSD 2-Clause "Simplified" License
      •6•8•3•0•Updated May 19, 2025May 19, 2025

    • otcetera

      Public
      C++20 lib for manipulations of phylogenetic trees and supertree operations
      C++
      •
      Other
      •3•4•38•0•Updated May 16, 2025May 16, 2025

    • chronosynth

      Public
      Match dates from chronograms in phylesystem to synthetic tree nodes
      Python
      •0•1•5•0•Updated Mar 7, 2025Mar 7, 2025

    • ws_wrapper

      Public
      OpenTree Web-Services Wrapper
      Python
      •0•1•2•1•Updated Feb 4, 2025Feb 4, 2025

    • germinator

      Public
      miscellaneous scripts and data for concerns that span more than one of the Open Tree code repositories: integration tests, system statistics, etc.
      Python
      •
      BSD 2-Clause "Simplified" License
      •7•23•41•1•Updated Nov 18, 2024Nov 18, 2024

    • phylesystem-0

      Public
      Yet another testing repository. This one is full size for performance testing. But still temporary.
      3•3•2•0•Updated Oct 4, 2024Oct 4, 2024

    • phylesystem-api

      Public
      API access to Open Tree of Life treestore
      Python
      •
      BSD 2-Clause "Simplified" License
      •4•11•60•0•Updated Jul 26, 2024Jul 26, 2024

    • git_wrap_opentree

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated May 27, 2024May 27, 2024

    • collections-0

      Public
      Collections of trees from the OpenTree datastore.
      BSD 2-Clause "Simplified" License
      •2•0•0•0•Updated Mar 5, 2024Mar 5, 2024

    • amendments-0

      Public
      Test data for taxonomic amendments API (peyotl)
      BSD 2-Clause "Simplified" License
      •2•0•0•0•Updated Oct 3, 2023Oct 3, 2023

    • eertgif

      Public
      experimental project. yet another pdf2newick converter
      Python
      •
      Other
      •0•1•0•0•Updated Sep 12, 2023Sep 12, 2023

    • otindex_ansible

      Public
      ansible playbook for installation of OpenTree otindex
      Jinja
      •
      BSD 2-Clause "Simplified" License
      •1•0•4•0•Updated Aug 4, 2023Aug 4, 2023

    • otindex

      Public
      opentree index using postgres and pyramid
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•23•0•Updated Aug 1, 2023Aug 1, 2023

    • deployed-systems

      Public
      A collection of current (and past) server configuration files for opentree components
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•0•1•0•Updated Mar 17, 2022Mar 17, 2022

    • taxomachine

      Public
      taxonomy graphdb
      Java
      •
      Other
      •4•7•26•2•Updated Jun 4, 2021Jun 4, 2021

    • test-ot-ws

      Public
      standalone test of web services
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•4•0•Updated Nov 13, 2020Nov 13, 2020