• ‘AlphaSim’ Software for breeding program simulation


    This computational software simulates strategies or methodologies defined by the user in plant and animal breeding programs with the aim of performing rapid, low-cost, and objective in silico comparison of breeding technologies. This software can simulate a wide range of mating designs, biotechnologies and selection strategies.

    Product details and features

    1. AlphaSim simulates breeding programs in a series of steps. For each step, the user defines very specific parameters according to their requirements. Different data are obtained, e.g., the user can obtain genetic values.
    2. Allows the simulation of multiple traits and/or environments, simulation of DH individuals in any given generation, evaluation of genome editing in breeding programs and choosing the selection strategy (truncation or optimal contribution)
    3. Includes a stop simulation process in any user-specified generation, import of third-party software data and merge different simulations to create a new merged population


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    1. AlphaSim generates three types of outputs directories: Chromosome, Selection and Simulated Data each with different types of results and data.
    2. Computational power depends on the type of simulation and the settings defined by the user. This could require one CPU core with 2GB of RAM to 12 CPU cores with 5 GB of RAM each. Time also differs depending on the type of simulation.

     

    Comments

    More information about this software is published in Faux et al., 2016. AlphaSim: software for breeding program simulation. The Plant Genome.



    Primary Users

    Breeders, students and researchers at public institutes and private seed companies. This software was designed for plant breeding programs but it can be used in animal breeding, human genetics and population genetics.

    Availability

    AlphaSim is available from http://www.alphagenes.roslin.ed.ac.uk/alphasuite/alphasim/. Material includes the compiled program for 64-bit Linux, Mac OSX, and Windows and the user manual. A user manual is included and a set of step-by-step examples

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