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DNAKit: A Comprehensive Toolkit for Efficient DNA Research
What is DNAKit?
DNAKit is a reproducible Python toolkit for DNA sequence analysis, positioned as an "RDKit for DNA." It covers standardization, sequence and annotation formats, basic operations, descriptors, pattern scanning, thermodynamics, fingerprints, similarity analysis, clustering and dataset splitting, comprehensive evaluation, molecular-biology simulation, and visualization. DNA foundation models can optionally be used for direct property prediction or to extract representations for k-means clustering.
Installation and quick start
Install the current release:
pip install dnakit==0.1.4
Install the optional VEP, ClinVar, dbSNP, gnomAD, dN/dS, and Golden Gate
backend with pip install "dnakit[external-tools]".
To expose DNAKit to an MCP-capable Agent, install dnakit[agent] and configure the
dnakit-mcp command in the Agent client.
To contribute to development, clone the repository and create the complete Conda environment:
conda env create -f environment-dev.yml
conda activate dnakit-dev
Then explore the feature tree.
Additional distribution platforms
The repository provides Bioconda and GNU Guix recipes
and a Galaxy Tool Shed wrapper.
These files target 0.1.1. Until they are reviewed and published by their respective platforms,
use the PyPI installation method above.
Documentation
The complete English documentation is available from the DNAKit documentation homepage, including the feature tree and FAQ.
Support and community
GitHub repository:
For questions, feedback, or suggestions, see:
Changelog
See CHANGELOG.md for release notes.
Citation
The DNAKit project paper has not yet been published. Cite the current version as:
DNAKit contributors. DNAKit 0.1.4, 2026. https://github.com/mapengsen/DNAKit
The paper has been submitted for publication, this section will be updated after the paper is published. When using specific algorithms,databases, or optional backends, cite their corresponding sources as well.
The working tree also provides bioinformatics Python APIs: native DNA encodings, generative metrics, statistics and specification-based optimization, plus optional format codecs and specialist alignment/NGS backends. Install these with python -m pip install -e ".[bio]".
1 maintainer
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