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recombination rate and maternal linkage disequilibrium     (LD) are estimated for pairs of biallelic markers such as single nucleotide     polymorphisms (SNPs) from progeny genotypes and sire haplotypes. The     implementation relies on paternal half-sib families. If maternal half-sib     families are used, the roles of sire/dam are swapped. Multiple families can     be considered. For parameter estimation, at least one sire has to be double     heterozygous at the investigated pairs of SNPs.    Based on recombination rates, genetic distances between markers can be     estimated. Markers with unusually large recombination rate to markers in     close proximity (i.e. putatively misplaced markers) shall be discarded in     this derivation.    A workflow description is attached as vignette.    *A pipeline is available at GitHub*    <https://github.com/wittenburg/hsrecombi>    Hampel, Teuscher, Gomez-Raya, Doschoris, Wittenburg (2018) \"Estimation of     recombination rate and maternal linkage disequilibrium in half-sibs\"     <doi:10.3389/fgene.2018.00186>.    Gomez-Raya (2012) \"Maximum likelihood estimation of linkage disequilibrium     in half-sib families\" 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