Generating samples under a Wright-Fisher neutral model of genetic variation

Generating samples under a Wright-Fisher neutral model of genetic variation

Received on August 8, 2001; revised and accepted on September 13, 2001 | Richard R. Hudson
The article introduces a Monte Carlo computer program written in C by Richard R. Hudson to generate samples from populations evolving according to a Wright–Fisher neutral model. The program assumes an infinite-sites mutation model and allows for recombination, gene conversion, symmetric migration among subpopulations, and various demographic histories. It uses the coalescent approximation to the Wright–Fisher model, which is accurate for small sample sizes relative to population size. The program can simulate samples with constant population size, without subpopulations, and without recombination or gene conversion. Additional complexities, such as recombination, gene conversion, migration, and changing population size, can be incorporated by specifying additional command-line arguments. The output includes the command line, random number generator seed, and the sampled data, including the number of polymorphic sites and their positions on a (0, 1) scale. The program is available for Linux, SunOS, and MacOsX, and the source code is provided at a specified URL.The article introduces a Monte Carlo computer program written in C by Richard R. Hudson to generate samples from populations evolving according to a Wright–Fisher neutral model. The program assumes an infinite-sites mutation model and allows for recombination, gene conversion, symmetric migration among subpopulations, and various demographic histories. It uses the coalescent approximation to the Wright–Fisher model, which is accurate for small sample sizes relative to population size. The program can simulate samples with constant population size, without subpopulations, and without recombination or gene conversion. Additional complexities, such as recombination, gene conversion, migration, and changing population size, can be incorporated by specifying additional command-line arguments. The output includes the command line, random number generator seed, and the sampled data, including the number of polymorphic sites and their positions on a (0, 1) scale. The program is available for Linux, SunOS, and MacOsX, and the source code is provided at a specified URL.
Reach us at info@study.space
[slides] Generating samples under a Wright-Fisher neutral model of genetic variation | StudySpace