Jan 7, 2014

Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences

BMC Bioinformatics
Tao YangTianhua Niu

Abstract

Coalescent simulation is pivotal for understanding population evolutionary models and demographic histories, as well as for developing novel analytical methods for genetic association studies for DNA sequence data. A plethora of coalescent simulators are developed, but selecting the most appropriate program remains challenging. We extensively compared performances of five widely used coalescent simulators - Hudson's ms, msHOT, MaCS, Simcoal2, and fastsimcoal, to provide a practical guide considering three crucial factors, 1) speed, 2) scalability and 3) recombination hotspot position and intensity accuracy. Although ms represents a popular standard coalescent simulator, it lacks the ability to simulate sequences with recombination hotspots. An extended program msHOT has compensated for the deficiency of ms by incorporating recombination hotspots and gene conversion events at arbitrarily chosen locations and intensities, but remains limited in simulating long stretches of DNA sequences. Simcoal2, based on a discrete generation-by-generation approach, could simulate more complex demographic scenarios, but runs comparatively slow. MaCS and fastsimcoal, both built on fast, modified sequential Markov coalescent algorithms to approxi...Continue Reading

  • References46
  • Citations8

References

  • References46
  • Citations8

Mentioned in this Paper

Computer Software
In Silico
Biologic Segmentation
Tandem Repeat Sequences
Genome
Dysequilibrium Syndrome
Genetics, Population
Recombination, Genetic
Genome Mapping
Genomics

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