XSim

XSim simulates sequence data and complex pedigree structures to model breeding programs and evaluate genomic selection and mating-scheme outcomes.

Key Features:

• Integration of Multiple Statistical Models: Integrates Genomic Best Linear Unbiased Prediction (GBLUP), Bayesian alphabets, and neural networks for genetic evaluation and prediction.
• Simulation of Sequence Data and Pedigrees: Simulates sequence-level genotypes and multi-generation pedigree structures to generate stochastic descendants for breeding scenarios.
• Modular Design for Complex Mating Schemes: Supports successive-generation simulations of intricate mating schemes, including crossbreeding in animal and plant populations and biotechnological methods such as double haploids and embryo transfer.
• Implementation in Julia: Implemented in the Julia programming language, combining scripting-language readability (R, Python) with computational speed comparable to C.
• Flexibility and Extensibility: Allows integration of diverse data sources and advanced statistical methods to accommodate varied experimental designs and analytical workflows.

Scientific Applications:

• Breeding program design and optimization: Enables design, evaluation, and optimization of plant and animal breeding programs through forward-time simulation of genotypes and pedigrees.
• Validation of genomic selection: Facilitates validation and assessment of genomic selection strategies by simulating selection decisions and their genetic consequences across generations.
• Assessment of mating plans and biotechnological interventions: Allows exploration of outcomes from complex mating plans and interventions such as double haploids and embryo transfer.
• Stochastic descendant simulation: Generates stochastic descendants using a drop-down strategy to evaluate variability and uncertainty in breeding outcomes.

Methodology:

Simulates genetic sequence data across generations using integrated statistical models (GBLUP, Bayesian alphabets, neural networks) within a modular architecture that applies diverse mating schemes and biotechnological methods.