AdmixSim 2

AdmixSim 2 simulates complex population admixture in a forward-time, individual-based framework to generate phased haplotype genomic data for evolutionary and population genetics analyses.

Key Features:

• Extended Wright-Fisher Model: Implements an extended Wright-Fisher model that incorporates gene flow, natural selection, recombination, and mutation.
• Versatile Population Simulation: Supports dioecious and monoecious populations and models both autosomes and sex chromosomes.
• Phased Haplotype Data Output: Produces phased haplotype data from empirical or previously simulated genomic inputs for downstream analysis.

Scientific Applications:

• Local Ancestry Inference: Provides simulated genomic segments to evaluate and develop local ancestry inference methods.
• Association Studies: Enables simulation of admixed populations for testing association analyses between genetic variants and traits.
• Comparative Analysis: Facilitates validation of simulated data against empirical datasets, as demonstrated with African American, Mexican, and Uyghur populations.

Methodology:

Uses an individual-based forward-time simulation built on an extended Wright-Fisher model that tracks genomes across successive generations and implements gene flow, natural selection, recombination, and mutation.