ArticleBMC bioinformatics2014
Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Human ancestries simulation and inference: a review of ancestral recombination graph-based approaches.Frontiers in bioinformatics · 2026Review
- Efficient ancestry and mutation simulation with msprime 1.0.Genetics · 2022Article
- Effects of Demographic History on the Detection of Recombination Hotspots from Linkage Disequilibrium.Molecular biology and evolution · 2018Article
- Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes.PLoS computational biology · 2016Article
- Approaching Long Genomic Regions and Large Recombination Rates with msParSm as an Alternative to MaCS.Evolutionary bioinformatics online · 2016Review
- Genetic data simulators and their applications: an overview.Genetic epidemiology · 2015Article
- Genetic simulation tools for post-genome wide association studies of complex diseases.Genetic epidemiology · 2015Article
- Cosi2: an efficient simulator of exact and approximate coalescent with selection.Bioinformatics (Oxford, England) · 2014Article
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3 authors.
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Abstract
backgroundCoalescent 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.
resultsWe 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 approximate standard coalescent, are much more efficient whilst keeping salient features of msHOT and Simcoal2, respectively. Our simulations demonstrate that they are more advantageous over other programs for a spectrum of evolutionary models. To validate recombination hotspots, LDhat 2.2 rhomap package, sequenceLDhot and Haploview were compared for hotspot detection, and sequenceLDhot exhibited the best performance based on both real and simulated data.
conclusionsWhile ms remains an excellent choice for general coalescent simulations of DNA sequences, MaCS and fastsimcoal are much more scalable and flexible in simulating a variety of demographic events under different recombination hotspot models. Furthermore, sequenceLDhot appears to give the most optimal performance in detecting and validating cross-over hotspots.
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