<p align="center">
<a href="https://github.com/jlsteenwyk/clipkit">
<img src="https://raw.githubusercontent.com/JLSteenwyk/ClipKIT/master/docs/_static/img/logo.jpg" alt="Logo" width="400">
</a>
<p align="center">
<a href="https://jlsteenwyk.com/ClipKIT/">Docs</a>
·
<a href="https://github.com/jlsteenwyk/clipkit/issues">Report Bug</a>
·
<a href="https://github.com/jlsteenwyk/clipkit/issues">Request Feature</a>
</p>
<p align="center">
<a href="https://github.com/JLSteenwyk/ClipKIT/actions" alt="Build">
<img src="https://img.shields.io/github/actions/workflow/status/JLSteenwyk/ClipKIT/ci.yml?branch=master">
</a>
<a href="https://codecov.io/gh/jlsteenwyk/clipkit" alt="Coverage">
<img src="https://codecov.io/gh/jlsteenwyk/clipkit/branch/master/graph/badge.svg?token=0J49I6441V">
</a>
<a href="https://github.com/jlsteenwyk/clipkit/graphs/contributors" alt="Contributors">
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<a href="https://bsky.app/profile/jlsteenwyk.bsky.social" target="_blank" rel="noopener noreferrer">
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</a>
<br />
<a href="https://pepy.tech/badge/clipkit">
<img src="https://static.pepy.tech/personalized-badge/clipkit?period=total&units=international_system&left_color=grey&right_color=blue&left_text=PyPi%20Downloads">
</a>
<a href="https://lbesson.mit-license.org/" alt="License">
<img src="https://img.shields.io/badge/License-MIT-blue.svg">
</a>
<a href="https://pypi.org/project/clipkit/" alt="PyPI - Python Version">
<img src="https://img.shields.io/pypi/pyversions/clipkit">
</a>
<a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001007">
<img src="https://zenodo.org/badge/DOI/10.1371/journal.pbio.3001007.svg">
</a>
</p>
</p>
<center><h2>Run <a href="https://clipkit.genomelybio.com/">ClipKIT in the browser</a> and leave the computing up to <a href="https://www.genomelybio.com/">us</a>!</h2></center>
<br />
ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others.<br /><br />
If you found clipkit useful, please cite *ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference*. Steenwyk et al. 2020, PLOS Biology. doi: [10.1371/journal.pbio.3001007](https://jlsteenwyk.com/publication_pdfs/2020_Steenwyk_etal_PLOS_Biology.pdf).
<br /><br />
---
<br />
This documentation covers downloading and installing ClipKIT. Details about each function as well as tutorials for using ClipKIT are available in the [online documentation](https://jlsteenwyk.com/ClipKIT/).
<br />
**Quick Start**
```shell
# install
pip install clipkit
# run
clipkit input.fa
```
<br />
**Installation**
**If you are having trouble installing ClipKIT, 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 clipkit
pip install clipkit
```
**Note, the virtual environment must be activated to use *clipkit*.**
After using ClipKIT, 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/ClipKIT.git
cd ClipKIT/
# 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 *clipkit*.**
<br />
To install via anaconda, execute the following command:
``` shell
conda install bioconda::clipkit
```
Visit here for more information: https://anaconda.org/bioconda/clipkit
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