PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process multiple sequence alignments and phylogenies for broad applications
If you found PhyKIT useful, please cite PhyKIT: a UNIX shell toolkit for processing and analyzing phylogenomic data. bioRxiv. doi: 10.1101/2020.10.27.358143.
Quick StartΒΆ
1) Installation
To install using pip, we strongly recommend building a virtual environment to avoid software dependency issues. To do so, execute the following commands:
# create virtual environment
python -m venv .venv
# activate virtual environment
source .venv/bin/activate
# install phykit
pip install phykit
Note, the virtual environment must be activated to use phykit.
After using PhyKIT, you may wish to deactivate your virtual environment and can do so using the following command:
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/PhyKIT.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:
Note, the virtual environment must be activated to use phykit.
2) Usage
Get the help message from PhyKIT:
phykit -h
- About
- Usage
- Alignment-based functions
- Tree-based functions
- Bipartition support statistics
- Branch length multiplier
- Collapse bipartitions
- Covarying evolutionary rates
- Degree of violation of the molecular clock
- Internal branch statistics
- Internode labeler
- Long branch score
- Patristic distances
- Polytomy testing
- Print tree
- Prune tree
- Rename tree tips
- Robinson-Foulds distance
- Spurious homolog identification
- Print tip labels
- Total tree length
- Treeness
- Alignment- and tree-based functions
- Tutorials
- FAQ
