Metadata-Version: 2.1
Name: clipkit
Version: 2.7.0
Summary: Alignment trimming software for phylogenetics.
Home-page: https://github.com/jlsteenwyk/clipkit
Author: Jacob L. Steenwyk
Author-email: jlsteenwyk@gmail.com
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE.md

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    <a href="https://jlsteenwyk.com/ClipKIT/">Docs</a>
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    ·
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    <p align="center">
        <a href="https://github.com/JLSteenwyk/ClipKIT/actions" alt="Build">
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        <a href="https://pepy.tech/badge/clipkit">
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        <a href="https://anaconda.org/bioconda/clipkit">
          <img src="https://img.shields.io/conda/dn/bioconda/clipkit?label=bioconda%20downloads" alt="Bioconda Downloads">
        </a>
        <a href="https://lbesson.mit-license.org/" alt="License">
            <img src="https://img.shields.io/badge/License-MIT-blue.svg">
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        <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>   
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</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
