cff-version: 1.2.0
message: "If you use Allelica or derived population-genetics visualizations from this repository, please cite this software, the upstream source, and the listed source references."
title: "Allelica: Hardy-Weinberg Population Genetics Visualizer"
type: software
authors:
  - alias: "khandelwalsumo-oss"
  - alias: "allaunthefox"
repository-code: "https://github.com/allaunthefox/Allelica"
url: "https://github.com/allaunthefox/Allelica"
abstract: >-
  Allelica is a Python-based Hardy-Weinberg population genetics visualizer for
  allele-frequency data, Hardy-Weinberg expected genotype-frequency estimates,
  and population-level comparisons across selected genes and traits. It is
  currently a bounded, educational and exploratory tool, not a clinical genetics
  system or evidence of causation for traits, adaptation, disease risk, or
  evolutionary mechanisms.
keywords:
  - Allelica
  - allele frequency
  - Hardy-Weinberg equilibrium
  - population genetics
  - genotype frequency
  - genetic variation
  - biological addressability
  - gnomAD
license: MIT
references:
  - type: software
    title: "Allelica upstream repository"
    authors:
      - alias: "khandelwalsumo-oss"
    repository-code: "https://github.com/khandelwalsumo-oss/Allelica"
    url: "https://github.com/khandelwalsumo-oss/Allelica"
    notes: >-
      Upstream source repository named by GitHub as the fork origin for this
      repository. Preserve this attribution when using or extending the fork.
  - type: webpage
    title: "Built a Hardy-Weinberg population genetics visualizer with real gnomAD data — looking for honest feedback (17 y/o, self taught)"
    authors:
      - alias: "Puzzled_Maximum7018"
    url: "https://www.reddit.com/r/bioinformatics/"
    notes: >-
      Reddit r/bioinformatics provenance page supplied by the fork maintainer as
      context for the original project goals, feedback, and limitations. The page
      frames Allelica as a first GitHub / high-school informatics project using
      Hardy-Weinberg expected genotype frequencies from allele-frequency data and
      asks for critique on biological validity. Treat this as provenance and
      review context, not as a scientific source or validation of the method.
      A canonical Reddit post permalink was not captured in the pasted source.
  - type: dataset
    title: "Genome Aggregation Database (gnomAD)"
    url: "https://gnomad.broadinstitute.org/"
    notes: >-
      Source database named in the project README for allele-frequency data.
      Users should cite the relevant gnomAD release and any underlying studies
      directly when performing scientific analyses. This entry records repository
      provenance only and is not a substitute for release-specific gnomAD citation.
  - type: article
    title: "A global reference for human genetic variation"
    authors:
      - family-names: "Karczewski"
        given-names: "Konrad J."
      - family-names: "Francioli"
        given-names: "Laurent C."
      - family-names: "Tiao"
        given-names: "Grace"
      - family-names: "Cummings"
        given-names: "Beryl B."
      - family-names: "Alföldi"
        given-names: "Jessica"
      - family-names: "Wang"
        given-names: "Qingbo"
      - family-names: "Collins"
        given-names: "Ryan L."
      - family-names: "Laricchia"
        given-names: "Kristen M."
      - family-names: "Ganna"
        given-names: "Andrea"
      - family-names: "Birnbaum"
        given-names: "Daniel P."
    journal: "Nature"
    year: 2020
    volume: 581
    pages: "434-443"
    doi: "10.1038/s41586-020-2308-7"
    url: "https://doi.org/10.1038/s41586-020-2308-7"
    notes: >-
      Canonical gnomAD reference for human genetic variation. Listed as a bounded
      data-source reference for Allelica's population-genetics visualizations.
  - type: article
    title: "Mendelian proportions in a mixed population"
    authors:
      - family-names: "Hardy"
        given-names: "G. H."
    journal: "Science"
    year: 1908
    volume: 28
    issue: 706
    pages: "49-50"
    doi: "10.1126/science.28.706.49"
    url: "https://doi.org/10.1126/science.28.706.49"
    notes: >-
      Original short note associated with the Hardy-Weinberg equilibrium baseline.
      Allelica uses this equilibrium as a baseline comparator, not as proof that
      real populations satisfy all equilibrium assumptions.
  - type: article
    title: "On the law of inheritance in man"
    authors:
      - family-names: "Weinberg"
        given-names: "Wilhelm"
    journal: "Jahreshefte des Vereins für vaterländische Naturkunde in Württemberg"
    year: 1908
    volume: 64
    pages: "368-382"
    notes: >-
      Historical source associated with the Hardy-Weinberg equilibrium principle.
      Included to document the mathematical baseline underlying Allelica.
notes: >-
  Project guardrail: VariantExists does not imply VariantMatters. Allele and
  Hardy-Weinberg expected genotype-frequency visualizations require population
  context, phenotype context, environmental assumptions, database provenance,
  sample size, uncertainty estimates, and evidence receipts before supporting
  biological interpretation. Hardy-Weinberg output should be treated as a baseline
  comparator when equilibrium assumptions may be violated. Reddit feedback in the
  supplied provenance page specifically flags hardcoded values, unclear extraction,
  ancestry/environment grouping ambiguity, lack of observed genotype comparison,
  and the need for sample sizes, uncertainty, and equilibrium/selection tests.