msHOT

msHOT simulates genetic variation by extending the coalescent simulator ms to incorporate multiple crossover and gene conversion hotspots within a genomic region, enabling modeling of complex recombination events.

Key Features:

• Multiple Hotspot Implementation: Simulates both crossover and gene conversion hotspots that may overlap between categories but are prohibited from overlapping within the same category (crossover vs crossover or gene conversion vs gene conversion).
• Coalescent-Based Simulation Framework: Extends the coalescent simulator ms to generate genetic variation data under specified recombination hotspot configurations.
• Enhanced Realism in Genetic Simulations: Models complex recombination events to better reflect the impact of hotspot activity on genetic diversity and linkage patterns.

Scientific Applications:

• Population Genetics Studies: Simulates hotspot-driven recombination to study population structure, evolutionary history, and effects of genetic drift.
• Phylogenetic Analysis: Models recombination landscapes to inform phylogeny construction and interpretation of species divergence in the presence of recombination.
• Genomic Research: Generates datasets that capture hotspot influence on mutation and recombination patterns for investigations of genome evolution and function.

Methodology:

Integrates crossover and gene conversion hotspots into the ms coalescent simulation framework to model recombination events.