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Welcome to Physcraper’s repository!

Build Status Documentation codecov pyOpenSci DOI NSF-1759846 NSF-1759838

Automated gene tree updating
with the Open Tree of Life

Use a phylogenetic tree and a DNA alignment to automatically find and add nucleotide sequences from a genetic database, to reproducibly improve and advance phylogenetic knowledge within a biological group.

Physcraper relies on taxonomic and phylogenetic resources and programmatic tools from the Open Tree of Life project.

Physcraper also leverages on programmatic tools from the TreeBASE project and NCBI, as well as multiple software projects listed as requirements below, to create an automatic and reproducible workflow for phylogenetics.

You are now on the code repository. Please refer to Physcraper’s documentation website for more details on:

🐹 🌴 🐸 🌾 🐼 🌷 🐙 🌼 🐳 🍄 🐜 🌵 🐟 🍁 🐃 🦠 🐚 🐛 :octocat:


If you use Physcraper, please cite:

  • Sánchez-Reyes, L.L., M. Kandziora, & E.J McTavish. (2021). Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life. BMC Bioinformatics 22, 355. doi:

  • Open Tree of Life, B. Redelings, L.L. Sanchez Reyes, K.A. Cranston, J. Allman, M.T. Holder, & E.J. McTavish. (2019). Open Tree of Life Synthetic Tree (Version 12.3). Zenodo. doi: 10.5281/zenodo.3937741


Physcraper is made available through the GNU General Public License v3.0


The tool is under active development in the McTavish Lab. Please post a GitHub issue here or contact if you need any help or have feedback.

Updating the README

The README.Rmd file generates the file, which in turn generates what is shown on Physcraper’s home page at its GitHub repository, and PyPI’s description.

To update from README.Rmd file, you need R and the rmarkdown package installed to run:

R -e 'rmarkdown::render("README.Rmd")'

The index.rst file that lives in the docs/source/ folder controls the home page at readthedocs, which is updated automatically as you push to GitHub.

To update any of these, you have to modify, as needed, README.Rmd and docs/source/index.rst, as well as the following .md files living in the docs/mds/ folder:

  •, aka, this file

To create new sections, you just need to create new .md files in docs/mds/ and make sure to add them to README.Rmd and docs/source/index.rst