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ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others.

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.

This documentation covers downloading and installing ClipKIT. Details about each function as well as tutorials for using ClipKIT are available in the online documentation.

Quick Start

# install
pip install clipkit
# run
clipkit input.fa

Installation

If you are having trouble installing ClipKIT, please contact the lead developer, Jacob L. Steenwyk, via email or twitter 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:

# 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:

# deactivate virtual environment
deactivate

Similarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands:

# 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:

# deactivate virtual environment
deactivate

Note, the virtual environment must be activated to use clipkit.

To install via anaconda, execute the following command:

conda install bioconda::clipkit

Visit here for more information: https://anaconda.org/bioconda/clipkit