Principle of an AlphaSim simulation illustrated using a pedigree structured in four burn-in generations and one selection generation for two traits characterized by an additive genetic model. (1) Haplotype sequences and an internal pedigree are simulated. (2) Haplotypes are recombined and dropped into the base generation of the pedigree. At this step, single-nucleotide polymorphisms (SNPs) and quantitative trait nucleotides (QTNs) are selected. (3) An effect is assigned to each QTN, and, for each individual of the base generation of the pedigree, genetic values are calculated and phenotypes simulated. (4) Haplotypes of the base generation are recombined and dropped into the burn-in generations of the pedigree successively. Similar to the base generation, genetic values are calculated and phenotypes simulated for each individual of the burn-in generations. (5) A selection generation is simulated according to the selection method and strategy as defined by the user.