fastsimcoal2

fastsimcoal2 performs continuous-time coalescent-based genetic simulations and maximum-likelihood inference of demographic parameters using the site frequency spectrum (SFS).

Key Features:

• Coalescent simulation framework: Operates within a continuous-time coalescent-based genetic simulation framework.
• Maximum-likelihood SFS inference: Uses a maximum-likelihood approach to estimate demographic parameters from the site frequency spectrum (SFS).
• Complex scenario handling: Supports description and simulation of complex demographic scenarios via an extended input file syntax.
• Multi-threading capability: Implements multi-threading to accelerate computation for large datasets and simulations.
• Population inbreeding modeling: Includes functionality to model inbreeding within populations.
• Efficient simulations: Optimized for simulating sparsely structured populations and large chromosomes.

Scientific Applications:

• Demographic history reconstruction: Reconstructs demographic histories from genetic data.
• Admixture and gene flow analysis: Analyzes admixture events and gene flow among populations.
• Bottleneck and expansion analysis: Models population bottlenecks and expansions to assess historical size changes.
• Migration and population structure modeling: Models migration and complex population structure in evolutionary scenarios.
• Hypothesis testing of historical dynamics: Enables testing hypotheses about historical population dynamics using simulated and inferred SFS.
• Parameter inference for genetic diversity: Estimates demographic parameters that inform interpretation of genetic diversity patterns.

Methodology:

Performs continuous-time coalescent-based genetic simulations, applies a maximum-likelihood approach to the site frequency spectrum (SFS), supports an extended input file syntax for complex demographic scenarios, and includes multi-threading while modeling inbreeding and simulating sparsely structured populations and large chromosomes.