.. image:: _static/img/logo.png :width: 55% :align: center :target: https://jlsteenwyk.com/PhyKIT ^^^^^ 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: |doiLink|_. .. _doiLink: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btab096/6131675?redirectedFrom=fulltext .. |doiLink| replace:: 10.1093/bioinformatics/btab096 Quick Start ----------- These two lines represent the simpliest method to rapidly install and run PhyKIT. .. code-block:: shell # 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: .. code-block:: shell # 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: .. code-block:: shell # deactivate virtual environment deactivate | Similarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands: .. code-block:: shell # 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: .. code-block:: shell # deactivate virtual environment deactivate **Note, the virtual environment must be activated to use phykit.** | To install via anaconda, execute the following command: .. code-block:: shell conda install bioconda::phykit Visit here for more information: https://anaconda.org/bioconda/phykit **2) Usage** Get the help message from PhyKIT: .. code-block:: shell phykit -h | ^^^^ .. toctree:: :maxdepth: 4 about/index usage/index tutorials/index change_log/index other_software/index frequently_asked_questions/index ^^^^