ArticleFrontiers in immunology2024
PyPop: a mature open-source software pipeline for population genomics.
Article in Frontiers in immunology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Ancient genomics study reveals low HLA diversity in eastern hunter-gatherers.Genome biology · 2026Article
- SNPio: a Python interface for population genomic data processing.BMC bioinformatics · 2026Article
- Article
- Signatures of pathogen-driven selection and Austronesian gene flow of Papua New Guinea HLA alleles.American journal of human genetics · 2026Article
- HLAtools, Searching Shared HLA Amino Acid Residue Prevalence, and the Global Frequency Browsers: New Computational Resources for Working With HLA Data and Visualizing Global Patterns of HLA Variation.International journal of immunogenetics · 2025Article
- High resolution class I HLA-A, -B, and -C diversity in Eastern and Southern African populations.Scientific reports · 2025Article
- HLA diversity and signatures of selection in the Maniq, a nomadic hunter-gatherer population in Southern Thailand.Immunogenetics · 2025Article
- PyPop: a mature open-source software pipeline for population genomics.Frontiers in immunology · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
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. Code available at: https://zenodo.org/records/10080668 and https://github.com/alexlancaster/pypop.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.