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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

1) Installation

To install, 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.


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

To deactivate your virtual environment, use the following command:

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.


To install via anaconda, execute the follwoing command:

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

2) Usage

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

clipkit <input>

Output file with the suffix “.clipkit”