To cite the 'hsphase' package in publications use:

Ferdosi, M. H., Kinghorn, B. P., van der Werf, J. H. J., Lee, Seung Hwan & Gondro, C. hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups. BMC Bioinformatics 15, 172 (2014)

Ferdosi, M. H., Kinghorn, B. P., van der Werf, J. H. J. & Gondro, C. Detection of recombination events, haplotype reconstruction and imputation of sires using half-sib SNP genotypes. Genetics Selection Evolution 46, 11 (2014)

Ferdosi, M. H., Boerner, V. A fast method for evaluating opposing homozygosity in large SNP data sets. Livestock Science Accepted (2014)

Ferdosi, M. H., Gondro, C. hsphase - an R package for identification of recombination events, pedigree and haplotype reconstruction and imputation using SNP data from half-sib families (2018) :vignette R package version 2.0.2

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 = {http://www.biomedcentral.com/1471-2105/15/172/abstract},
    doi = {10.1186/1471-2105-15-172},
    language = {en},
    number = {1},
    urldate = {2014-06-07},
    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 = {http://www.gsejournal.org/content/46/1/11/abstract},
    doi = {10.1186/1297-9686-46-11},
    language = {en},
    number = {1},
    urldate = {2014-06-07},
    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 = {46},
    copyright = {2014 Ferdosi et al.; licensee {BioMed} Central Ltd.},
    issn = {1297-9686},
    url = {http://www.gsejournal.org/content/46/1/11/abstract},
    doi = {10.1186/1297-9686-46-11},
    language = {en},
    number = {1},
    urldate = {2014-06-07},
    journal = {Livestock Science},
    author = {Mohammad H Ferdosi and Vinzent Boerner},
    month = {feb},
    year = {2014},
    note = {{PMID:} 24495596},
    pages = {11},
  }

  @Manual{,
    title = {hsphase -- an R package for identification of
      recombination events, pedigree and haplotype reconstruction and
      imputation using SNP data from half-sib },
    language = {en},
    author = {Mohammad H Ferdosi and Cedric Gondro},
    year = {2018},
    note = {R package vignette version R package version 2.0.2},
  }