AlphaDrop beta

AlphaDrop beta simulates sequence, single nucleotide polymorphism (SNP), phased allele, genotype, and phenotype data within specified pedigree structures for genomic selection and genome-wide association study (GWAS) research.

Key Features:

• Flexible Simulation Capabilities: Allows definition of historical population structures and recent pedigree configurations to model complex genetic scenarios.
• Phased Alleles and Genotypes: Simulates sequence data and SNP-phased alleles and genotypes.
• Quantitative Trait Loci (QTL) Effects: Enables specification of the distribution of QTL effects for studies of additive genetic influence.
• Breeding Values Simulation: Simulates breeding values for use in genomic selection analyses.
• Pre-specified Pedigrees: Supports input of pre-defined pedigree structures to replicate specific breeding programs or population histories.
• Public Data Availability: Provides ten replicate datasets from a representative livestock genomic selection scenario that are publicly available for reproducibility and comparison.

Scientific Applications:

• Genomic Selection Studies: Model breeding programs, assess selection strategies, and predict genetic gains across generations.
• GWAS Simulations: Generate datasets with controlled QTL effects and population structures to validate GWAS methodologies and statistical models.
• Educational Purposes: Provide example datasets and simulation scenarios for teaching genomic data simulation and analysis techniques.

Methodology:

Uses the MaCS (Markov Chain Simulator) algorithm to drop simulated haplotypes through pedigrees, with configurable historical population structures, pedigree configurations, and QTL effect distributions.