Amber Biology LLC, Cambridge, MA, United States.
Ronin Institute, Montclair, NJ, United States.
Front Immunol. 2024 Apr 2;15:1378512. doi: 10.3389/fimmu.2024.1378512. eCollection 2024.
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.
Python 群体遗传学（PyPop）是一个软件包，用于处理基因型和等位基因数据，并对高度多态性的多位点基因型数据进行大规模群体遗传分析。特别是，PyPop 可以检验数据是否符合哈迪-温伯格平衡预期，进行选择的埃文斯-沃特森检验，估计单倍型频率，测量连锁不平衡，并检验显著性。执行这些检验的标准化方法是当代进化生物学和群体遗传学研究的关键，这些检验也是疾病关联遗传研究的核心。在此，我们发布了 PyPop 1.0.0，这是该软件包的一个重大新版本，它使用更强大的 GitHub 基础设施实现了新功能，并通过行业标准的 Python 包索引进行分发。新功能包括实现非对称连锁不平衡度量，以及特别受到免疫遗传学研究社区关注的，支持现代命名法，包括用冒号分隔的等位基因名称，并改进了元分析功能，用于聚合多个群体的输出。代码可在以下网址获取：https://zenodo.org/records/10080668 和 https://github.com/alexlancaster/pypop。
