To cite the 'hsphase' package in publications use:

Ferdosi MH, Kinghorn BP, van der Werf JH, Lee SH, Gondro C (2014). “hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups.” BMC Bioinformatics, 15(1), 172. ISSN 1471-2105, doi:10.1186/1471-2105-15-172, https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-172.

Ferdosi MH, Kinghorn BP, van der Werf JH, Gondro C (2014). “Detection of recombination events, haplotype reconstruction and imputation of sires using half-sib SNP genotypes.” Genetics Selection Evolution, 46(1), 11. ISSN 1297-9686, doi:10.1186/1297-9686-46-11, PMID: 24495596, https://gsejournal.biomedcentral.com/articles/10.1186/1297-9686-46-11.

Ferdosi MH, Boerner V (2014). “A fast method for evaluating opposing homozygosity in large SNP data sets.” Livestock Science, 166(1), 35-37. ISSN 1871-1413, doi:10.1186/1297-9686-46-11, PMID: 24495596, https://doi.org/10.1016/j.livsci.2014.05.026.

Ferdosi MH, Gondro C (2025). hsphase – an R package for identification of recombination events, pedigree and haplotype reconstruction and imputation using SNP data from half-sib families. R package vignette version R package version 2.0.4.

Corresponding BibTeX entries:

  @Article{,
    title = {hsphase: an R package for pedigree reconstruction,
      detection of recombination events, phasing and imputation of
      half-sib family groups},
    volume = {15},
    copyright = {http://creativecommons.org/licenses/by/2.0/},
    issn = {1471-2105},
    shorttitle = {hsphase},
    url =
      {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-172},
    doi = {10.1186/1471-2105-15-172},
    language = {en},
    number = {1},
    journal = {BMC Bioinformatics},
    author = {Mohammad H Ferdosi and Brian P Kinghorn and Julius HJ
      {van der Werf} and Seung Hwan Lee and Cedric Gondro},
    month = {jun},
    year = {2014},
    pages = {172},
  }

  @Article{,
    title = {Detection of recombination events, haplotype
      reconstruction and imputation of sires using half-sib SNP
      genotypes},
    volume = {46},
    copyright = {2014 Ferdosi et al.; licensee BioMed Central Ltd.},
    issn = {1297-9686},
    url =
      {https://gsejournal.biomedcentral.com/articles/10.1186/1297-9686-46-11},
    doi = {10.1186/1297-9686-46-11},
    language = {en},
    number = {1},
    journal = {Genetics Selection Evolution},
    author = {Mohammad H Ferdosi and Brian P Kinghorn and Julius HJ
      {van der Werf} and Cedric Gondro},
    month = {feb},
    year = {2014},
    note = {PMID: 24495596},
    pages = {11},
  }

  @Article{,
    title = {A fast method for evaluating opposing homozygosity in
      large SNP data sets.},
    volume = {166},
    copyright = {2014 Ferdosi et al.},
    issn = {1871-1413},
    url = {https://doi.org/10.1016/j.livsci.2014.05.026},
    doi = {10.1186/1297-9686-46-11},
    language = {en},
    number = {1},
    journal = {Livestock Science},
    author = {Mohammad H Ferdosi and Vinzent Boerner},
    month = {feb},
    year = {2014},
    note = {PMID: 24495596},
    pages = {35-37},
    doi = {10.1186/1297-9686-46-11},
  }

  @Manual{,
    title = {hsphase -- an R package for identification of
      recombination events, pedigree and haplotype reconstruction and
      imputation using SNP data from half-sib families},
    author = {Mohammad H Ferdosi and Cedric Gondro},
    year = {2025},
    note = {R package vignette version R package version 2.0.4},
  }