Repositories list

• AvesData

  Public
  Data deposit for Aves synthetic tree

  HTML

  •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

• AvesTreeCode

  Public
  Python

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Oct 16, 2024Oct 16, 2024

• mctavishlab.github.io

  Public
  HTML

  •1•2•0•0•Updated Jun 3, 2024Jun 3, 2024

• OpenTreeCLO

  Public
  Linking data between ebird and open tree

  Jupyter Notebook

  •0•0•1•0•Updated May 9, 2024May 9, 2024

• GradPhylo

  Public
  UC Merced QSB/ES 244

  0•6•0•0•Updated May 1, 2024May 1, 2024

• jupyter_OpenTree_tutorials

  Public
  Jupyter Notebook

  •0•0•0•0•Updated May 18, 2023May 18, 2023

• GBIF-Biodiverse-OpenTree

  Public
  Linking data between GBIF, Biodiverse, and Open Tree of Life

  Python

  •

  GNU Affero General Public License v3.0

  •0•2•0•0•Updated Dec 2, 2022Dec 2, 2022

• collab-paper

  Public
  McTavish Lab collab paper on usage of Phsycraper https://github.com/McTavishLab/physcraper

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Nov 7, 2022Nov 7, 2022

• extensiphy

  Public
  Pipeline to place taxa in a sequence alignment and phylogeny using NGS reads

  Python

  •

  GNU General Public License v3.0

  •2•2•2•0•Updated Aug 24, 2022Aug 24, 2022

• BIO144

  Public
  Files for BIO144, Phylogenetics

  HTML

  •0•1•0•0•Updated May 26, 2022May 26, 2022

• physcraper

  Public
  Welcome to Physcraper’s repository! Automatic gene tree updating using the Open Tree of Life.

  pythonbioinformaticsbiology

  Python

  •

  GNU General Public License v3.0

  •6•13•36•0•Updated May 13, 2022May 13, 2022

• R_OpenTree_tutorials

  Public
  Tutorials to use Open Tree of Life services using R.

  HTML

  •

  Other

  •1•1•0•0•Updated May 4, 2022May 4, 2022

• data-science-research

  Public
  HTML

  •

  Other

  •0•0•0•0•Updated Apr 20, 2022Apr 20, 2022

• rotl

  Public
  Interface to Open Tree of Life API

  R

  •

  Other

  •18•0•0•0•Updated Jan 24, 2022Jan 24, 2022

• OT2020

  Public
  Data exploration

  Jupyter Notebook

  •2•0•0•0•Updated Oct 26, 2021Oct 26, 2021

• datelifedocker

  Public
  Dockerfile to set up DateLife server. I hope.

  Dockerfile

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Oct 21, 2021Oct 21, 2021

• extensiphy_fork

  Public
  Pipeline to place taxa in a sequence alignment and phylogeny using NGS reads

  Python

  •2•3•3•0•Updated Oct 1, 2021Oct 1, 2021

• chronosynth_api_sandbox

  Public
  Python

  •0•0•0•0•Updated Sep 24, 2021Sep 24, 2021

• pyopensci.github.io

  Public
  This is the website for pyOpenSci. Contributions welcome!!

  SCSS

  •

  MIT License

  •61•0•0•0•Updated Sep 16, 2021Sep 16, 2021

• R_OpenTree_tutorials_fork

  Public
  Tutorials to use Open Tree of Life services using R.

  HTML

  •

  Other

  •2•0•0•0•Updated Sep 15, 2021Sep 15, 2021

• physcraper_ms

  Public
  first physcraper manuscript

  HTML

  •0•0•0•0•Updated Aug 11, 2021Aug 11, 2021

• ropentree

  Public
  Tools to streamline OpenTree of Life workflows

  R

  •0•0•0•0•Updated Jun 15, 2021Jun 15, 2021

• SummerGenomics

  Public
  Jupyter Notebook

  •1•2•0•0•Updated May 20, 2021May 20, 2021

• physcraperex

  Public
  Visualization of Physcraper Examples

  R

  •0•0•0•0•Updated Apr 6, 2021Apr 6, 2021

• Human-application-Dplus

  Public
  Python

  •1•0•0•0•Updated Sep 25, 2020Sep 25, 2020

• physcraper_example

  Public
  R

  •0•0•5•0•Updated Aug 4, 2020Aug 4, 2020

• biodiversity_next

  Public
  Python

  •0•1•0•0•Updated Dec 29, 2019Dec 29, 2019

• OpenTree-SSB2020-site

  Public
  HTML

  •

  Other

  •0•0•0•0•Updated Dec 28, 2019Dec 28, 2019

• OpenTreeHelpers

  Public
  Python wrappers for OpenTree Apis

  0•0•0•0•Updated Dec 5, 2019Dec 5, 2019

• opentree_helpers

  Public
  Pull OpenTree helpers out of physcraper for easier install

  0•0•0•0•Updated Nov 12, 2019Nov 12, 2019