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PhyKIT is a UNIX shell toolkit for processing and analyzing phylogenomic data.
If you found PhyKIT useful, please cite PhyKIT: a UNIX shell toolkit for processing and analyzing phylogenomic data. bioRxiv. doi: 10.1101/2020.10.27.358143.
This documentation covers downloading and installing PhyKIT. Details about each function as well as tutorials for using PhyKIT are available in the online documentation.
Installation
To install, use the following commands:
pip install phykit
To install from source, use the following commands:
git clone https://github.com/JLSteenwyk/PhyKIT.git
cd PhyKIT/
make install
If you run into permission errors when executing make install, create a virtual environment for your installation:
git clone https://github.com/JLSteenwyk/PhyKIT.git
cd PhyKIT/
python -m venv .venv
source .venv/bin/activate
make install
Note, the virtual environment must be activated to use phykit.
To test phykit installation, launch the help message
phykit -h
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