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hsphase

hsphase

hsphase is a tool to detect recombination events, phasing, genotype imputation, and to reconstruct pedigrees. The hsphase algorithm uses a genetic data structure within half-sib livestock to classify recombination events. It can also run directly on sequence data.

Topic

Population genetics

Details

  • Operation: Phasing; Imputation
  • Software interface: Command-line user interface; Library
  • Language: C++;R
  • Operating system: Microsoft Windows
  • License: GNU GPL v3+
  • Cost: Free
  • Version name: 2.0.0
  • Maturity: Stable
  • Credit: the Next-Generation BioGreen 21 Program, Rural Development Administration (RDA), Republic of Korea, Australian Research Council Discovery Project.
  • Contact: Cedric Gondro cgondro2 _at_ une.edu.au | Mohammad Ferdosi mferdosi _at_ myune.edu.au
  • Collection: -

Publications

Ferdosi MH, Kinghorn BP, van der Werf JH, Lee SH, Gondro C "hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups." BMC Bioinformatics. 2014 Jun 7;15:172. https://doi.org/10.1186/1471-2105-15-172
PMID: 24906803
PMCID: PMC4069276

Ferdosi MH, Kinghorn BP, van der Werf JH, Gondro C "Detection of recombination events, haplotype reconstruction and imputation of sires using half-sib SNP genotypes" Genet Sel Evol. 2014 Feb 4;46:11. https://doi.org/10.1186/1297-9686-46-11
PMID: 24495596
PMCID: PMC3996164

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