msms

msms simulates genetic variation in structured populations incorporating selection at a single diploid locus to model demographic, migration, and selective scenarios for studying selective sweeps and local adaptation.

Key Features:

• Structured Population Modeling: Retains the demographic models available in ms, supporting multiple demes with arbitrary migration patterns, population growth and decay, and events such as population splits and merges.
• Selection Modeling: Incorporates selection at a single diploid locus with support for deme- and time-dependent selection to model hard and soft selective sweeps and local adaptation.
• Compatibility and Extensibility: Produces output and accepts command conventions compatible with ms and is architected for extension to additional models.
• Performance: Maintains performance comparable to ms despite incorporating selection into coalescent simulations.

Scientific Applications:

• Power Studies: Enables assessment of the power of genetic tests under varied demographic and selective scenarios.
• Analytical Comparisons: Facilitates comparison between theoretical predictions and simulated data for validation of evolutionary models.
• Approximated Bayesian Computation (ABC): Generates datasets for parameter inference in complex population-genetic models used in ABC frameworks.

Methodology:

Uses a coalescent-based approach extended with forward simulations to model deme- and time-dependent selection at a single diploid locus.