To cite the 'RZooRoH' package and its model in publications, please use:

N.S. Forneris, P. Faux, M. Gautier and T. Druet (2026). Updating the RZooRoH Package for the Analysis of Inbreeding, Identity-By-Descent and Relatedness From Genomic Data. Molecular Ecology Resources, 26(6):e70186.<doi:10.1111/1755-0998.70186>

T. Druet and M. Gautier (2022). A hidden Markov model to estimate homozygous-by-descent probabilities associated with nested layers of ancestors. Theor Popul Biol, 145:38-51.<doi:10.1016/j.tpb.2022.03.001>

The ZooRoH model and its properties were first described in:

T. Druet and M. Gautier (2017). A model-based approach to characterize individual inbreeding at both global and local genomic scales. Molecular Ecology, 26:5820-5841.<doi:10.1111/mec.14324>

Extension to IBD and kinship analyses were first introduced in (see the RZooRoH update paper above for further details):

N.S. Forneris, M. Bosse, M. Gautier and T. Druet (2025). Genomic Prediction of Individual Inbreeding Levels for the Management of Genetic Diversity in Populations With Small Effective Size. Molecular Ecology Resources, 25(4):e14068.<doi:10.1111/1755-0998.14068>

The previous RZooRoH package (prior to version 4) is described in:

A.R. Bertrand, N.K. Kadri, L. Flori, M. Gautier and T. Druet (2019). RZooRoH: an R package to characterize individual genomic autozygosity and identify homozygous-by-descent segments. Methods in Ecology and Evolution, 10(6):860-866.<doi:10.1111/2041-210X.13167>

Corresponding BibTeX entries:

  @Article{,
    author = {Natalia S. Forneris and Pierre Faux and Mathieu Gautier
      and Tom Druet},
    title = {Updating the RZooRoH Package for the Analysis of
      Inbreeding, Identity-By-Descent and Relatedness From Genomic
      Data.},
    journal = {Molecular Ecology Resources},
    year = {2026},
    volume = {26},
    number = {6},
    pages = {e70186},
    doi = {10.1111/1755-0998.70186},
  }

  @Article{,
    author = {Tom Druet and Mathieu Gautier},
    title = {A hidden Markov model to estimate homozygous-by-descent
      probabilities associated with nested layers of ancestors.},
    journal = {Theoretical Population Biology},
    year = {2022},
    volume = {145},
    pages = {38-51},
    doi = {10.1016/j.tpb.2022.03.001},
  }

  @Article{,
    author = {Tom Druet and Mathieu Gautier},
    title = {A model-based approach to characterize individual
      inbreeding at both global and local genomic scales.},
    journal = {Molecular Ecology},
    year = {2017},
    volume = {26},
    number = {20},
    pages = {5820-5841},
    doi = {10.1111/mec.14324},
  }

  @Article{,
    author = {Natalia Soledad Forneris and Mirte Bosse and Mathieu
      Gautier and Tom Druet},
    title = {Genomic Prediction of Individual Inbreeding Levels for the
      Management of Genetic Diversity in Populations With Small
      Effective Size.},
    journal = {Molecular Ecology Resources},
    year = {2025},
    volume = {25},
    number = {4},
    pages = {e14068},
    doi = {10.1111/1755-0998.14068},
  }

  @Article{,
    author = {Amandine Bertrand and Naveen Kadri and Laurence Flori and
      Mathieu Gautier and Tom Druet},
    title = {RZooRoH: an R package to characterize individual genomic
      autozygosity and identify homozygous-by-descent segments.},
    journal = {Methods in Ecology and Evolution},
    year = {2019},
    volume = {10},
    number = {6},
    pages = {860-866},
    doi = {10.1111/2041-210X.13167},
  }