Metadata-Version: 2.4
Name: phykit
Version: 2.1.0
Home-page: https://github.com/jlsteenwyk/phykit
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: Topic :: Scientific/Engineering
Description-Content-Type: text/markdown
License-File: LICENSE.md
Requires-Dist: biopython>=1.82
Requires-Dist: numpy>=1.24.0
Requires-Dist: scipy>=1.11.3
Requires-Dist: scikit-learn>=1.4.2
Requires-Dist: cython
Requires-Dist: tqdm>=4.65.0
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: license-file
Dynamic: requires-dist

<p align="center">
  <a href="https://github.com/jlsteenwyk/phykit">
    <img src="https://raw.githubusercontent.com/JLSteenwyk/PhyKIT/master/docs/_static/img/phykit_logo.png" alt="Logo" width="400">
  </a>
  <p align="center">
    <a href="https://jlsteenwyk.com/PhyKIT/">Docs</a>
    ·
    <a href="https://github.com/jlsteenwyk/phykit/issues">Report Bug</a>
    ·
    <a href="https://github.com/jlsteenwyk/phykit/issues">Request Feature</a>
  </p>
    <p align="center">
        <a href="https://github.com/JLSteenwyk/PhyKIT/actions" alt="Build">
            <img src="https://img.shields.io/github/actions/workflow/status/JLSteenwyk/PhyKIT/ci.yml?branch=master">
        </a>
        <a href="https://codecov.io/gh/jlsteenwyk/phykit" alt="Coverage">
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        </a>
        <a href="https://github.com/jlsteenwyk/phykit/graphs/contributors" alt="Contributors">
            <img src="https://img.shields.io/github/contributors/jlsteenwyk/phykit">
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        <a href="https://bsky.app/profile/jlsteenwyk.bsky.social" target="_blank" rel="noopener noreferrer">
          <img src="https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky&logoColor=fff">
        </a>
        <br />
        <a href="https://pepy.tech/badge/phykit">
          <img src="https://static.pepy.tech/personalized-badge/phykit?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/phykit/" alt="PyPI - Python Version">
            <img src="https://img.shields.io/pypi/pyversions/phykit">
        </a>
        <a href="https://academic.oup.com/bioinformatics/article-abstract/37/16/2325/6131675?redirectedFrom=fulltext">
          <img src="https://zenodo.org/badge/DOI/10.1093/bioinformatics/btab096.svg">
        </a>
    </p>
</p>

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
```
