Metadata-Version: 2.1
Name: clipkit
Version: 1.1.3
Summary: Alignment trimming software for phylogenetics.
Home-page: https://github.com/jlsteenwyk/clipkit
Author: Jacob L. Steenwyk
Author-email: jlsteenwyk@gmail.com
License: UNKNOWN
Description: <p align="center">
          <a href="https://github.com/jlsteenwyk/clipkit">
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            <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>
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                <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">
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                <a href="https://github.com/JLSteenwyk/ClipKIT/actions" alt="Build">
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                        alt="follow on Twitter">
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        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://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001007).
        <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 />
        
        **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 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 *clipkit*.**
        
        <br />
        
        To install via anaconda, execute the follwoing command:
        
        ``` shell
        conda install -c jlsteenwyk clipkit
        ```
        Visit here for more information: https://anaconda.org/jlsteenwyk/clipkit
        
Platform: UNKNOWN
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering
Description-Content-Type: text/markdown
