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 algorithm for accurate phylogenomic inference. bioRxiv. doi: 10.1101/2020.06.08.140384.
To install, use the following commands:
pip install clipkit
To install from source, use the following commands:
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 use ClipKIT in its simpliest form, execute the following command:
Output file with the suffix “.clipkit”