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CI status Documentation Python 3.10+ MIT license

PyPI version Bioconda recipe Galaxy wrapper GNU Guix package

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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==0.1.3

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:

github.com/mapengsen/DNAKit

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 0.1.3, 2026. https://github.com/mapengsen/DNAKit

This section will be updated after the paper is published. When using specific algorithms, databases, or optional backends, cite their corresponding sources as well.

Project links

Data verified by PyPI on Sep 3, 2026
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  • Released:
Newer release available (0.1.4)

1 maintainer

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Avatar for mapengsen from gravatar.com mapengsen

Credits

Author: DNAKit contributors

GitHub Statistics

Data verified by PyPI on Sep 3, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License expression

MIT
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Requires

Python >=3.10

Provides Extra

dev docs viz io validation external-tools agent neural neural-caduceus neural-enformer neural-evo2

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