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.
Population genetics
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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