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:
- installation instructions using an Anaconda or a Virtualenv Python virtual environment,
- function usage,
- finding and choosing a starting dataset,
- running a full analysis,
- visualizing and analysing results,
- real life examples, and
- instructions for developers, and specifically on how to update this readme.
🐹 🌴 🐸 🌾 🐼 🌷
🐙 🌼 🐳 🍄 🐜 🌵 🐟
🍁 🐃 🦠 🐚 🐛 
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:
doi.org/10.1186/s12859-021-04274-6.
- 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 ejmctavish@ucmerced.edu if you need any help or have feedback.
The README.Rmd file generates the README.md file, which in turn
generates what is shown on Physcraper’s home page at its GitHub
repository, and
PyPI’s description.
To update README.md 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:
- intro-badges.md
- intro-logo.md
- intro-part1.md
- citation.md
- license.md
- contact.md
- updating-the-readme.md, 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