ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes those that display characteristics poor phylogenetic signal.

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.

Quick Start

These two lines represent the simpliest method to rapidly install and run ClipKIT.

# install
pip install clipkit
# run
clipkit input.fa

Below are more detailed instructions, including alternative installation methods.

1) Installation

To help ensure ClipKIT can be installed using your favorite workflow, we have made ClipKIT available from pip, source, and the anaconda cloud.

Install from pip

To install from pip, use 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.

Install from source

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.

git clone https://github.com/JLSteenwyk/ClipKIT.git
cd ClipKIT/
make install

If you run into permission errors when executing make install, create a virtual environemnt for your installation:

git clone https://github.com/JLSteenwyk/ClipKIT.git
cd ClipKIT/
python -m venv venv
source venv/bin/activate
make install

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

Install from anaconda

To install via anaconda, execute the following command:

conda install bioconda::clipkit

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

2) Usage

To use ClipKIT in its simpliest form, execute the following command:

clipkit <input>

Output file with the suffix “.clipkit”