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Code availability
The scikit-bio project’s official website is https://scikit.bio. The source code of scikit-bio is licensed under a BSD-3 licensed and hosted at the public GitHub repository https://github.com/scikit-bio/scikit-bio. Version 0.7.0 of the source code has been permanently archived at the Zenodo repository at https://zenodo.org/records/15988672. The scikit-bio software package is distributed free of charge via PyPI (https://pypi.org/project/scikit-bio/) and conda-forge (https://anaconda.org/conda-forge/scikit-bio). Comprehensive documentation of scikit-bio, including guidelines, API references and example usages, are available at the official website. A structured list of scikit-bio tutorials is available at https://github.com/scikit-bio/scikit-bio-tutorials.
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Acknowledgements
We thank a large number of community contributors for their valuable inputs to the scikit-bio project. The development of scikit-bio is currently funded by the US Department of Energy, Office of Science, under award DE-SC0024320.
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Contributions
R.K. and J.G.C. initiated the scikit-bio project in 2013; J.G.C. led the project from 2013 to 2023; and Q.Z. has led the project since 2023. M.A., D.M., J.T.M. and Q.Z. comprise the current core development team of scikit-bio. M.A. is responsible for the maintenance of scikit-bio. R.K. provides advisory support. J.G.C. provides consulting. All authors have made significant contributions to the development of scikit-bio, including but not limited to code, documentation, test data and educational materials. Q.Z. and M.A. led the writing of the manuscript, with input from other authors. All authors reviewed and approved the final manuscript.
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Competing interests
R.K. is a scientific advisory board member and consultant for BiomeSense, Inc., and has equity in and receives income from the company. He is a scientific advisory board member for and has equity in GenCirq. He is a consultant for and receives income from DayTwo. He has equity in and acts as a consultant for Cybele. He is a co-founder of Biota, Inc., and has equity in the company. He is a cofounder of Micronoma, and has equity in and is a scientific advisory board member for the company. The terms of these arrangements have been reviewed and approved by the University of California, San Diego, in accordance with its conflict of interest policies. D.M. is a consultant for BiomeSense, Inc., and has equity in and receives income from the company. The terms of these arrangements have been reviewed and approved by the University of California, San Diego, in accordance with its conflict of interest policies. Y.V.-B. is a full-time employee for BiomeSense, Inc., and has equity in and receives income from the company. J.R.R. is a full-time employee for One Codex, Inc., and has equity in and receives income from the company. J.G.C. and E.B. have equity in and receive income from Cymis Benefit Corp. J.C.A.’s contribution to this work was completed before he joined Amazon Robotics. All other authors declare no competing interests.
Peer review
Peer review information
Nature Methods thanks Zewen Kelvin Tuong, who co-reviewed with Amos Choo, and Ralf Gommers and Tyler Reddy for their contributions to the peer review of this work.
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Supplementary Information
Supplementary Tables 1–3.
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Aton, M., McDonald, D., Cañardo Alastuey, J. et al. Scikit-bio: a fundamental Python library for biological omic data analysis. Nat Methods (2025). https://doi.org/10.1038/s41592-025-02981-z
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DOI: https://doi.org/10.1038/s41592-025-02981-z
