CITATION.cff

cff-version: 1.3.0
message: >-
  If you use this software, please cite both the software itself, as well as the
  article Lancaster AK et al. (2024) <a
  href=\"https://doi.org/10.3389/fimmu.2024.1378512\">PyPop: A mature
  open-source software pipeline for population genomics</a>. <i>Front.
  Immunol.</i> <b>15</b>:1378512. doi: 10.3389/fimmu.2024.1378512
abstract: >-
  <p>PyPop for Population Genomics (<a href=\"http://pypop.org/\">PyPop</a>) 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).&nbsp;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
  values (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.</p>
authors:
  - family-names: Lancaster
    given-names: Alexander K.
    orcid: https://orcid.org/0000-0002-0002-9263
    affiliation:
      - Amber Biology LLC
      - name: Institute for Globally Distributed Open Research and Education
        ror: https://ror.org/01643wd06
  - family-names: Nelson
    given-names: Mark P.
    affiliation:
      - name: University of California, Berkeley
        ror: https://ror.org/01an7q238
  - family-names: Single
    given-names: Richard
    orcid: https://orcid.org/0000-0001-6054-6505
    affiliation:
      - name: University of Vermont
        ror: https://ror.org/0155zta11
  - family-names: Solberg
    given-names: Owen
    orcid: https://orcid.org/0000-0003-3060-9709
  - family-names: Tsai
    given-names: Yingsu
    affiliation:
      - name: University of California, Berkeley
        ror: https://ror.org/01an7q238
    orcid: https://orcid.org/0009-0006-0162-6066
  - family-names: Meyer
    given-names: Diogo
    orcid: https://orcid.org/0000-0002-7155-5674
    affiliation:
      - name: University of São Paulo
        ror: https://ror.org/036rp1748
  - family-names: Webster
    given-names: Gordon
    affiliation:
      - name: Amber Biology LLC
      - name: Ronin Institute
        ror: https://ror.org/04awze035
    orcid: https://orcid.org/0009-0009-2862-0467
  - family-names: Mariani
    given-names: Michael P.
    orcid: https://orcid.org/0000-0001-5852-0517
    affiliation:
      - name: Mariani Systems LLC
      - name: University of Vermont
        ror: https://ror.org/0155zta11
  - family-names: Sochat
    given-names: Vanessa
    orcid: https://orcid.org/0000-0002-4387-3819
    affiliation:
      - name: Lawrence Livermore National Laboratory
        ror: https://ror.org/041nk4h53
  - family-names: Kornel
    given-names: Karl
    orcid: https://orcid.org/0000-0001-5847-5330
    affiliation: Stanford Research Computing Center
  - family-names: Spaaks
    given-names: Jurriaan H.
    orcid: https://orcid.org/0000-0002-7064-4069
    affiliation:
      - name: Netherlands eScience Center
        ror: https://ror.org/00rbjv475
  - family-names: Mack
    given-names: Steven J.
    orcid: https://orcid.org/0000-0001-9820-9547
    affiliation:
      - name: University of California, San Francisco
        ror: https://ror.org/043mz5j54
  - family-names: Thomson
    given-names: Glenys
    orcid: https://orcid.org/0000-0001-5235-4159
    affiliation:
      - name: University of California, Berkeley
        ror: https://ror.org/01an7q238
title: 'PyPop: Python for Population Genomics'
repository-artifact: https://pypi.org/project/pypop-genomics/
repository-code: https://github.com/alexlancaster/pypop/
license: GPL-2.0-or-later
version: v1.2.0
type: software
url: http://pypop.org/
identifiers:
  - description: PyPop homepage
    type: url
    value: http://pypop.org/
    relation: IsSupplementedBy
  - description: PyPop documentation
    type: url
    value: http://pypop.org/docs
    relation: IsDocumentedBy
  - description: Previous Tissue Antigens (2007) publication
    type: doi
    value: 10.1111/j.1399-0039.2006.00769.x
    relation: Continues
  - description: Preprint version of TA (2007) publication
    type: url
    value: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4369784
    relation: Continues
  - description: GitHub tag for repository
    type: url
    value: https://github.com/alexlancaster/pypop/tree/v1.2.0
    relation: IsSupplementTo
  - description: PyPI package
    type: url
    value: https://pypi.org/project/pypop-genomics/1.2.0
    relation: IsSourceOf
  - description: DOI concept identifier for all versions of PyPop
    type: doi
    value: 10.5281/zenodo.10080667
    relation: IsVersionOf
keywords:
  - population genetics
  - population genomics
  - bioinformatics
  - computational biology
  - evolutionary biology
  - Human leukocyte antigen
  - Major histocompatibility complex
  - HLA
  - MHC
doi: 10.5281/zenodo.14799509