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PhyKIT is a UNIX shell toolkit for processing and analyzing phylogenomic data.<br /><br />
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](https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btab096/6131675).
<br /><br />
---
This documentation covers downloading and installing PhyKIT. Details about each function as well as tutorials for using PhyKIT are available in the <a href="https://jlsteenwyk.com/PhyKIT/">online documentation</a>.
<br />
**Quick Start**
```shell
# install
pip install phykit
# run
phykit <function> <input file>
```
<br />
**Installation** <br />
**If you are having trouble installing PhyKIT, please contact the lead developer, Jacob L. Steenwyk, via [email](https://jlsteenwyk.com/contact.html) or [twitter](https://twitter.com/jlsteenwyk) 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:
```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:
```shell
# deactivate virtual environment
deactivate
```
<br />
Similarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands:
```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:
```shell
# deactivate virtual environment
deactivate
```
**Note, the virtual environment must be activated to use phykit.**
<br />
To install via anaconda, execute the following command:
```shell
conda install bioconda::phykit
```
Visit here for more information:
https://anaconda.org/bioconda/phykit
<br />
To test phykit installation, launch the help message
```shell
phykit -h
```
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