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</p>
BioKIT is a UNIX shell toolkit for processing molecular sequence data.<br /><br />
If you found biokit useful, please cite the following: *BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data*. Genetics. doi: [10.1101/2021.10.02.462868](https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyac079/6583183).
<br /><br />
---
This documentation covers downloading and installing BioKIT. Details about each function as well as tutorials for using BioKIT are available in the <a href="https://jlsteenwyk.com/BioKIT/">online documentation</a>.
<br />
**Installation** <br />
**If you are having trouble installing BioKIT, 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 biokit
pip install jlsteenwyk-biokit
```
**Note, the virtual environment must be activated to use biokit.**
After using biokit, 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/BioKIT.git
cd biokit/
# 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 biokit.**
<br />
To install via anaconda, execute the following command:
```shell
conda install -c jlsteenwyk jlsteenwyk-biokit
```
Visit here for more information:
https://anaconda.org/JLSteenwyk/jlsteenwyk-biokit
<br />
To test biokit installation, launch the help message
```shell
biokit -h
```
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