PhyKIT, a toolkit for the UNIX shell environment with numerous functions that process multiple sequence alignments and phylogenies for broad applications

If you found PhyKIT useful, please cite PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data. Bioinformatics. doi: 10.1093/bioinformatics/btab096.

Quick Start¶

These two lines represent the simpliest method to rapidly install and run PhyKIT.

# install
pip install phykit
# run
phykit -h

1) Installation

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 phykit
pip install phykit

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

After using PhyKIT, 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/PhyKIT.git
cd PhyKIT/
# 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 phykit.

To install via anaconda, execute the following command:

conda install bioconda::phykit

Visit here for more information: https://anaconda.org/bioconda/phykit

2) Usage

Get the help message from PhyKIT:

phykit -h