AlphaSim offers the user a high degree of simulation flexibility making it a useful tool for designing and optimizing new breeding strategies using newly developed technologies. This allows a user to perform plant or animal breeding simulations in any species using a wide range of strategies. AlphaSim combines features from three previous simulation packages, AlphaDrop ( Hickey and Gorjanc, 2012), AlphaSimPlant, and AlphaMPSim ( Hickey et al., 2014), with new features to form a comprehensive software package capable of simulating a wide range of mating designs, biotechnologies, and selection strategies. T his paper introduces AlphaSim, a software package for simulating breeding programs. AlphaSim can also be used in animal breeding, human genetics, and population genetics.AlphaSim is flexible, computationally efficient, and easy to use for a wide range of possible scenarios.AlphaSim allows breeders and researchers to simulate genomic data with specific user criteria.In conclusion, AlphaSim is a flexible and computationally efficient software package to simulate biotechnology enhanced breeding programs with the aim of performing rapid, low-cost, and objective in silico comparison of breeding technologies. By combining the options, a user can simulate simple or complex breeding programs with several generations, variable population structures and variable breeding decisions over time. AlphaSim also includes restart functionalities, which increase its flexibility by allowing the simulation process to be paused so that the parameters can be changed or to import an externally created pedigree, trial design, or results of an analysis of previously simulated data. 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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