Admixem

Admixem simulates admixture and selection dynamics in forward time to model genetic evolution in admixed populations.

Key Features:

• Forward-Time Simulation: Operates in a forward-time simulation framework to model genetic changes over generations.
• Admixture Modeling: Models admixture events with user-defined admixture proportions and timings to represent gene flow between populations.
• Selection Simulation: Implements selection via user-defined fitness functions and mating-preference probabilities to model positive and negative selection on specific genomic sites.
• Genomic Landscape Customization: Allows specification of realistic genomic landscapes including neutral single nucleotide polymorphisms (SNPs) and loci under selection.
• General Population Simulation: Can be applied as a general population simulator beyond admixture-specific scenarios.
• Technical Specifications: Implemented in C++ with OpenMP parallelization and targeted to 64-bit Linux/Unix-like platforms.

Scientific Applications:

• Population Genetics: Analyze the genetic consequences of admixture events and selection on population structure and allele frequencies.
• Genomic Studies: Investigate how selection acts across genomic landscapes and identify loci under selection.
• Evolutionary Biology: Simulate evolutionary scenarios to examine mechanisms driving genetic diversity and adaptation.

Methodology:

Simulations are driven by user-defined fitness functions, mating-preference probabilities, and input genomic landscapes (neutral SNPs and selected sites) within a forward-time simulation framework.