Table of Contents:
  • The site frequency spectrum (SFS)
  • Wright-Fisher with no mutations
  • The coalescent process (backwards Wright-Fisher)
  • Adding mutations
  • The expected SFS
  • Distance between heterozygote sites
  • Wright-Fisher with recombination
  • The ancestral recombination graph (ARG)
  • Probability tree heights along the sequence
  • Expected histogram for distance between heterozygote sites
  • Simulation study: detecting a bottleneck