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 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 PhyKIT/
# 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 -c jlsteenwyk clipkit
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”