ms

ms simulates samples from populations evolving under the Wright-Fisher neutral model using Monte Carlo methods and an infinite-sites mutation model to study genetic drift, allele frequency changes, and neutral genetic variation.

Key Features:

• Monte Carlo simulation: Uses stochastic simulation to generate population genetic samples under specified evolutionary models.
• Wright-Fisher neutral model: Simulates population evolution under the Wright-Fisher neutral framework to model genetic drift and allele frequency dynamics.
• Infinite-sites mutation model: Implements the infinite-sites mutation model so each new mutation occurs at a unique genomic site without recurrent mutations.
• Recombination: Simulates recombination events to represent meiotic shuffling of genetic material.
• Gene conversion: Simulates gene conversion events in which one DNA sequence replaces a homologous sequence.
• Symmetric migration among subpopulations: Supports symmetric migration to model gene flow between defined subpopulations.
• Demographic histories: Accommodates configurable demographic histories, including population size changes such as bottlenecks and expansions.
• Sampling properties: Generates samples for evaluating the sampling properties of any sample statistic under neutral evolutionary models.

Scientific Applications:

• Genetic drift and allele frequency dynamics: Study stochastic changes in allele frequencies under the Wright-Fisher neutral model.
• Mutation pattern analysis: Examine patterns of polymorphism under the infinite-sites mutation model.
• Recombination and linkage studies: Assess the effects of recombination and gene conversion on linkage disequilibrium and haplotype structure.
• Gene flow and population structure: Investigate how symmetric migration among subpopulations influences genetic diversity and population structure.
• Demographic inference and testing: Simulate bottlenecks, expansions, and other demographic scenarios to evaluate their impact on genetic variation.
• Statistical sampling evaluation: Explore the sampling distributions and properties of summary statistics under neutral evolutionary models.

Methodology:

Performs Monte Carlo simulation of the Wright-Fisher neutral model with an infinite-sites mutation model and explicit simulation of recombination, gene conversion, symmetric migration among subpopulations, and configurable demographic histories.