qdiv: Microbial Diversity Analysis Toolkit
qdiv is a Python toolkit for microbial diversity analysis, built around the robust and intuitive Hill number framework.
Features
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Data Management: Load and validate data from multiple formats (CSV/TSV, FASTA, Newick). Functions for subsetting, rarefaction, merging, renaming, tree pruning, and more.
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Diversity analysis: Compute multiple alpha and beta diversity metrics based on the Hill number framework.
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Statistical methods: Integrate diversity metrics using the Hill number framework into null models (Raup–Crick, NRI, NTI), ordinations (PCoA, db-RDA), PERMANOVA, and Mantel tests.
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Visualization: Heatmaps, ordinations, and diversity plots, and more.
Installation
pip install qdiv
Optional acceleration (Numba)
Some functions in the sequence_comparisons module support compilation via Numba. Installing qdiv with the optional accelerate extra enables faster sequence distance computations.
pip install qdiv[accelerate]
Documentation
Full documentation is available at: https://qdiv.readthedocs.io
Licence
From version 4.0.0, qdiv is licensed under the https://opensource.org/licenses/BSD-3-Clause. Previous versions were released under the GNU General Public License v3.0 (GPL-3.0).
Contributing
Contributions are welcome! Please read the CONTRIBUTING.md for details on:
- How to report bugs
- How to request new features
- How to submit pull requests
Support
If you need help with qdiv:
- Browse existing issues
- If needed, open a support issue. See SUPPORT.md.
Code of Conduct
To ensure a welcoming environment, this project follows the standards outlined in the CODE_OF_CONDUCT.md. All contributors are expected to uphold this code.
Citation
If you use qdiv in your research, please cite:
Modin. (2026). qdiv: A Python package for microbial ecology analysis using the Hill number framework. Journal of Open Source Software, 11(121), 10089. https://doi.org/10.21105/joss.10089.
Download the citation here:
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