PyPop: a mature open-source software pipeline for population genomics
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 E...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-04-01
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| Series: | Frontiers in Immunology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2024.1378512/full |
| _version_ | 1827298251654561792 |
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| author | Alexander K. Lancaster Alexander K. Lancaster Alexander K. Lancaster Richard M. Single Steven J. Mack Vanessa Sochat Michael P. Mariani Michael P. Mariani Gordon D. Webster Gordon D. Webster |
| author_facet | Alexander K. Lancaster Alexander K. Lancaster Alexander K. Lancaster Richard M. Single Steven J. Mack Vanessa Sochat Michael P. Mariani Michael P. Mariani Gordon D. Webster Gordon D. Webster |
| author_sort | Alexander K. Lancaster |
| collection | DOAJ |
| description | 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 |
| first_indexed | 2024-04-24T15:10:58Z |
| format | Article |
| id | doaj.art-be39c84a44ef4727a564110bf1bb8b67 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-04-24T15:10:58Z |
| publishDate | 2024-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-be39c84a44ef4727a564110bf1bb8b672024-04-02T11:01:25ZengFrontiers Media S.A.Frontiers in Immunology1664-32242024-04-011510.3389/fimmu.2024.13785121378512PyPop: a mature open-source software pipeline for population genomicsAlexander K. Lancaster0Alexander K. Lancaster1Alexander K. Lancaster2Richard M. Single3Steven J. Mack4Vanessa Sochat5Michael P. Mariani6Michael P. Mariani7Gordon D. Webster8Gordon D. Webster9Amber Biology LLC, Cambridge, MA, United StatesRonin Institute, Montclair, NJ, United StatesInstitute for Globally Distributed Open Research and Education (IGDORE), Cambridge, MA, United StatesDepartment of Mathematics and Statistics, University of Vermont, Burlington, VT, United StatesDepartment of Pediatrics, University of California, San Francisco, Oakland, CA, United StatesLivermore Computing, Lawrence Livermore National Laboratory, Livermore, CA, United StatesDepartment of Mathematics and Statistics, University of Vermont, Burlington, VT, United StatesMariani Systems LLC, Hanover, NH, United StatesAmber Biology LLC, Cambridge, MA, United StatesRonin Institute, Montclair, NJ, United StatesPython 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/pypophttps://www.frontiersin.org/articles/10.3389/fimmu.2024.1378512/fullHLAMHCpopulation genomicssoftwarebioinformatics |
| spellingShingle | Alexander K. Lancaster Alexander K. Lancaster Alexander K. Lancaster Richard M. Single Steven J. Mack Vanessa Sochat Michael P. Mariani Michael P. Mariani Gordon D. Webster Gordon D. Webster PyPop: a mature open-source software pipeline for population genomics Frontiers in Immunology HLA MHC population genomics software bioinformatics |
| title | PyPop: a mature open-source software pipeline for population genomics |
| title_full | PyPop: a mature open-source software pipeline for population genomics |
| title_fullStr | PyPop: a mature open-source software pipeline for population genomics |
| title_full_unstemmed | PyPop: a mature open-source software pipeline for population genomics |
| title_short | PyPop: a mature open-source software pipeline for population genomics |
| title_sort | pypop a mature open source software pipeline for population genomics |
| topic | HLA MHC population genomics software bioinformatics |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2024.1378512/full |
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