SelSim

SelSim simulates DNA polymorphism data under selection in recombining regions using Monte Carlo coalescent models to evaluate the effects of a single bi-allelic site subject to natural selection.

Key Features:

• Simulation modes: Implements both stochastic Monte Carlo simulations and deterministic approximations of natural selection.
• Coalescent framework: Generates genealogies and simulates variation within the coalescent framework for recombining regions.
• Selected site modeling: Models a single bi-allelic site under natural selection within recombining regions.
• Mutation models: Incorporates various mutation models to simulate neutral genetic variation surrounding the selected site.
• Exploration of selection effects: Enables examination of how different selection models and strengths influence patterns of genetic diversity.

Scientific Applications:

• Statistical analysis: Produces realistic DNA polymorphism datasets to aid in detection and characterization of natural selection from empirical data.
• Method development: Provides simulated data for development and validation of new methods to detect natural selection.

Methodology:

Performs Monte Carlo simulations within the coalescent framework in recombining regions, modeling a single bi-allelic selected site with either stochastic or deterministic selection approximations and incorporating various mutation models for neutral variation.