Published February 1, 2024 | Version Preprint v1
Preprint Open

PyPop: A mature open-source software pipeline for population genomics

  • 1. Amber Biology LLC
  • 2. ROR icon Ronin Institute
  • 3. ROR icon Institute for Globally Distributed Open Research and Education
  • 4. ROR icon University of Vermont
  • 5. ROR icon University of California, San Francisco
  • 6. ROR icon Lawrence Livermore National Laboratory
  • 7. Mariani Systems LLC


Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well. Here, we present PyPop 1.0.0, a new major release of the package, which implements new features using the more robust infrastructure of GitHub, and is distributed via the industry-standard Python Package Index. New features include implementation of the asymmetric linkage disequilibrium measures and, of particular interest to the immunogenetics research communities, support for modern nomenclature, including colon-delimited allele names, and improvements to meta-analysis features for aggregating outputs for multiple populations.


This preprint is under consideration with a journal.

Technical info



Files (933.0 kB)

Name Size Download all
755.0 kB Preview Download
141.5 kB Preview Download
36.5 kB Preview Download

Additional details

Related works

Software: 10.5281/zenodo.10080667 (DOI)