MaCS

MaCS simulates genomic sequences under a Markovian coalescent with recombination to generate haplotypes across large chromosomal regions for population genetics and GWAS applications.

Key Features:

• Efficient Simulation: MaCS employs a Markovian process to spatially simulate genealogies across chromosomes and scales linearly with sample size and sequence length.
• Comprehensive Demographic Modeling: MaCS supports a wide range of demographic scenarios comparable to MS (MicroSimulator), enabling modeling of complex population histories.
• Performance Metrics: MaCS has been evaluated against other simulators and demonstrates superior efficiency and accuracy in simulating haplotypes under arbitrary models of population history.
• Practical Applications: MaCS generates realistic genomic data for structured populations and reproduces linkage disequilibrium measures that closely resemble real genotype data, supporting GWAS analyses.

Scientific Applications:

• Genome-wide association studies (GWAS): MaCS produces genotype and haplotype datasets for structured populations to support GWAS analyses.
• Population genetics studies: MaCS enables exploration of genetic diversity and evolutionary history under varied demographic scenarios.
• Linkage disequilibrium and haplotype analysis: MaCS simulates LD measures and haplotype patterns that closely resemble real genotype data.

Methodology:

MaCS uses a Markovian coalescent process that spatially simulates genealogies across chromosomes with recombination and implements an algorithm that scales linearly with sample size and sequence length.