The following scripts were originally distributed with simuPOP in the scripts directory. They have been used for different research topics and can serve as examples on how to use simuPOP in real-world applications. Note that the documentations may be incorrect and there may be bugs in the script. Please examine the scripts carefully before you use them for any particular task.

Published papers that make use of simuPOP

These scripts were written for particular research papers. I have tried to update them so that they could run correctly under the current simuPOP version.

  • simuCDCV simulation for Reich’s paper: On the allelic spectrum of human disease plus migration and complexity of the common disease. (for publication Peng and Kimmel, Genetics, 2007)
  • simuComplexDisease generate dataset for common complex disease with certain number of disease susceptibility loci. (for publication Peng et al, PLoS Genetics, 2007)
  • simuGxE simulate samples with complex human diseases by evolving one or more HapMap populations forward in time. This scripts makes use of many forward time simulation techniques to make sure that simulated samples resemble the HapMap populations closely. (a paper that describes this method has been submitted)

Rapid re-implementation for published papers

  • Calafell2001 Haplotype Evolution and Linkage Disequilibrium: A simulation Study
  • Balloux2002 Statistical properties of population differentiation estimators under stepwise mutation in a finite island model
  • Abdallah2003 Linkage disequlibrium fine mapping of quantitative trait loci: A simulation study

Script for fun (research related)

These scripts are written in simuPOP for various purposes. They can be useful examples for your research.

  • simuForward Evolve a population forward in time, introduce a disease mutant at given generation.
  • simuRecHotSpot Look if recombination hotspot could be generated through even recombination.
  • simuNeutralSNPs Simulates the evolution of a chromosome with SNP markers, under the influence of mutation, migration, recombination and population size change.
  • landscapeGenetics A landscape genetics simulation with different selection forces on X and Y axis and epistasis.