AlphaMPSim

AlphaMPSim simulates genetic data for multi-parent populations to enable fine-scale analysis of genome structure and marker-trait associations in designs such as recombinant inbred lines.

Key Features:

• Flexible Simulation Capabilities: Simulates alternative crossing designs for multi-parent populations, accommodates traits with diverse genetic architectures, and supports biallelic markers at densities from sparse panels to full genomic sequences.
• Integration with Coalescent Simulations: Integrates with coalescent simulation programs such as MaCS to accept or generate large pools of founder haplotypes.
• Automatic Generation of Diverse Founders: Automatically generates founder lines from supplied or generated haplotypes and permits comparison of designs derived from varied pedigrees.
• Identity by Descent Tracking: Tracks the identity by descent status of alleles within the pedigree throughout simulations.
• Compatibility with Analysis Packages: Produces output files compatible with widely used analysis packages in R.

Scientific Applications:

• Genome-Wide Association Studies (GWAS): Simulates diverse genetic backgrounds to evaluate marker-trait associations and inform GWAS design and interpretation.
• Genetic Architecture Analysis: Enables investigation of complex trait genetic architectures by simulating varied genetic architectures and marker densities.
• Pedigree-Based Genetic Research: Assesses how different pedigrees and crossing designs influence trait inheritance using full allele descent tracking.

Methodology:

Integrates user-supplied or coalescent-generated founder haplotypes (e.g., via MaCS) into explicit multi-parent crossing designs and performs full identity-by-descent tracking of alleles to enable comparison of alternative pedigree scenarios.