It integrates biotechnologies such as doubled-haploids (DHs) and gene editing and allows the user to simulate multiple traits and multiple environments, specify recombination hot spots and cold spots, specify gene jungles and deserts, perform genomic predictions, and apply optimal contribution selection. The program is flexible in terms of historical population structure and diversity, recent pedigree structure, trait architecture, and selection strategy. AlphaSim simulates breeding programs in a series of steps: (i) simulate haplotype sequences and pedigree (ii) drop haplotypes into the base generation of the pedigree and select single-nucleotide polymorphism (SNP) and quantitative trait nucleotide (QTN) (iii) assign QTN effects, calculate genetic values, and simulate phenotypes (iv) drop haplotypes into the burn-in generations and (v) perform selection and simulate new generations. AlphaSim enables the simulation of multiple aspects of breeding programs with a high degree of flexibility. This paper describes AlphaSim, a software package for simulating plant and animal breeding programs.
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