CoaSim

CoaSim simulates genetic data using Monte Carlo coalescent models to generate datasets under equilibrium and non-equilibrium demographic scenarios for interpreting intra-specific sequence and polymorphism surveys and for planning and evaluating association studies.

Key Features:

• Monte Carlo coalescent engine: Performs Monte Carlo simulations of genetic data under coalescent processes.
• Equilibrium and non-equilibrium models: Implements both equilibrium and non-equilibrium demographic coalescent models.
• Guile Scheme scripting: Uses the Guile version of the Scheme scripting language to specify models and control simulations with user-modifiable scripts.
• Model-based dataset generation: Generates simulated datasets under diverse evolutionary models for direct comparison with empirical data.

Scientific Applications:

• Interpretation of polymorphism surveys: Enables interpretation of large-scale intra-specific sequence and polymorphism surveys by providing simulated expectations.
• Association study planning and evaluation: Supports planning and evaluation of association studies and evaluation of association mapping methods via simulated data.
• Parametric bootstrapping: Facilitates parametric bootstrapping to assess statistical significance under specified evolutionary models.
• Marker design and selection: Assists in the design and selection of genetic markers tailored to specific research questions.

Methodology:

Performs Monte Carlo simulations of genetic data under equilibrium and non-equilibrium coalescent processes, generates simulated datasets under specified evolutionary models, compares simulated datasets with empirical data to test significance of evolutionary factors, and uses Guile Scheme scripts to specify and modify simulation workflows.