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.

Quick Start

1) Installation

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.

2) Usage

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

clipkit <input>

Output file with the suffix “.clipkit”