Abstract: Various embodiments simulate crossover events on a chromosome. In one embodiment, a number Y of positions to be selected on a simulated chromosome is determined. Y positions j1, . . . , jy on the simulated chromosome are selected. A crossover event is placed at one or more of the positions j1, . . . , jy based on Y>0. An additional number Y? of positions j?1, . . . , j?y to be selected on the simulated chromosome is determined. Y? additional positions j?1, . . . , j?y on the simulated chromosome are selected. An additional crossover event is placed at one or more of the additional positions j?1, . . . , j?y based on Y?>0 and a neighborhood t associated with the one or more of the additional positions j?1, . . . , j?y being free of crossover events. A set of crossover event locations is identified based on the one or more of the positions j1, . . . , jy and additional positions j?1, . . . , j?y at which a crossover event has been placed.

Abstract: Various embodiments simulate crossover events on a chromosome. In one embodiment, a number Y of positions to be selected on a simulated chromosome is determined. Y positions j1, . . . , jy on the simulated chromosome are selected. A crossover event is placed at one or more of the positions j1, . . . , jy based on Y>0. An additional number Y? of positions j?1, . . . , j?y to be selected on the simulated chromosome is determined. Y? additional positions j?1, . . . , j?y on the simulated chromosome are selected. An additional crossover event is placed at one or more of the additional positions j?1, . . . , j?y based on Y?>0 and a neighborhood t associated with the one or more of the additional positions j?1, . . . , j?y being free of crossover events. A set of crossover event locations is identified based on the one or more of the positions j1, . . . , jy and additional positions j?1, . . . , j?y at which a crossover event has been placed.

Abstract: A system for reconstructing haplotypes from genotype data includes a memory, a processor, and a reconstruction module. The reconstruction module is configured to access a set of progeny genotype data including n progenies encoded with m genetic markers. A first set of parent haplotypes associated with a first parent of the n progenies and a second set of parent haplotypes associated with a second parent of the n progenies are identified based on at least the set of progeny genotype data. An agglomerate data structure including a collection of sets of haplotype sequences characterizing the n progenies is constructed based on the set of progeny genotype data and the first and second sets of parent haplotypes. Each set of haplotype sequences includes a number of crossovers equal to a total minimum number of observable crossovers in the n progenies.

Abstract: Various embodiments reconstruct haplotypes from genotype data. In one embodiment, a set of progeny genotype data comprising n progenies encoded with m genetic markers is accessed. A first set of parent haplotypes associated with a first parent of the n progenies and a second set of parent haplotypes associated with a second parent of the n progenies are identified based on at least the set of progeny genotype data. A total minimum number of observable crossovers in the n progenies is determined. An agglomerate data structure comprising a collection of sets of haplotype sequences characterizing the n progenies is constructed based on the set of progeny genotype data and the first and second sets of parent haplotypes. Each set of haplotype sequences includes a number of crossovers equal to the total minimum number of observable crossovers in the n progenies.