Published February 25, 2024 | Version v1.0.2
Software Open

PyPop: Python for Population Genomics

  • 1. Amber Biology LLC
  • 2. ROR icon Ronin Institute
  • 3. ROR icon University of California, Berkeley
  • 4. ROR icon University of Vermont
  • 5. ROR icon Universidade de São Paulo
  • 6. Mariani Systems LLC
  • 7. ROR icon Lawrence Livermore National Laboratory
  • 8. Stanford Research Computing Center
  • 9. ROR icon Netherlands eScience Center
  • 10. ROR icon University of California, San Francisco


PyPop for Population Genomics (PyPop) is a Python program for processing genotype and allele data and running population genetic analyses, including conformity to Hardy-Weinberg expectations; tests for balancing or directional selection; estimates of haplotype frequencies and measures and tests of significance for linkage disequilibrium (LD). Output of analyses are stored in XML format for maximum downstream flexibility. PyPop also has an internal facility for additionally aggregating the output XML and generating output tab-separated (TSV) files, as well as default plain text files for each population. Although it can be run on any kind of genotype data, it has additional support for analyzing population genotype with allelic nomenclature from the human leukocyte antigen (HLA) region.


If you use this software, please cite both the software itself, as well as the article Lancaster AK, Single RM, Mack SJ, Sochat V, Mariani MP, Webster GD. (2024) “PyPop: A mature open-source software pipeline for population genomics.” Front. Immunol. 15:1378512 doi: 10.3389/fimmu.2024.1378512

Technical info

Main website:

Development is on GitHub:

Binary packages are available on PyPI:


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Additional details


National Institutes of Health
14th International HLA &Immunogenetics Workship (HIWS) 1R13AI066863-01
National Institutes of Health
Population Genetics of the HLA Region 2R01GM035326-13A1
National Institutes of Health
Bioinformatics Integration Support Contract for Immune-Mediated Diseases N01AI40076-11-0-2
National Institutes of Health