README.md

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OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees.

If you found orthosnap useful, please cite OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees. Steenwyk et al. 2022, PLOS Biology. doi: 10.1371/journal.pbio.3001827.

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This documentation covers downloading and installing orthosnap. Details about orthosnap usage including a tutorial are available on our online documentation.

Installation

If you are having trouble installing orthosnap, please contact the lead developer, Jacob L. Steenwyk, via email or twitter to get help.

To install using pip, we strongly recommend building a virtual environment to avoid software dependency issues. To do so, execute the following commands:

# create virtual environment
python -m venv .venv
# activate virtual environment
source .venv/bin/activate
# install orthosnap
pip install orthosnap

Note, the virtual environment must be activated to use orthosnap.

After using orthosnap, you may wish to deactivate your virtual environment and can do so using the following command:

# deactivate virtual environment
deactivate

Similarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands:

# download
git clone https://github.com/JLSteenwyk/orthosnap.git
cd orthosnap/
# create virtual environment
python -m venv .venv
# activate virtual environment
source .venv/bin/activate
# install
make install

To deactivate your virtual environment, use the following command:

# deactivate virtual environment
deactivate

Note, the virtual environment must be activated to use orthosnap.

To install via anaconda, execute the follwoing command:

conda install -c jlsteenwyk orthosnap

Visit here for more information: https://anaconda.org/jlsteenwyk/orthosnap