ArticleBMC bioinformatics2008
Fregene: simulation of realistic sequence-level data in populations and ascertained samples.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
39 citing papers in PubMed.
- CoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination.BMC bioinformatics · 2020Article
- Rapid Identification of Rainbow Trout Adulteration in Atlantic Salmon by Raman Spectroscopy Combined with Machine Learning.Molecules (Basel, Switzerland) · 2019Article
- GeneEvolve: a fast and memory efficient forward-time simulator of realistic whole-genome sequence and SNP data.Bioinformatics (Oxford, England) · 2017Article
- SimBac: simulation of whole bacterial genomes with homologous recombination.Microbial genomics · 2016Article
- XSim: Simulation of Descendants from Ancestors with Sequence Data.G3 (Bethesda, Md.) · 2015Article
- Genetic data simulators and their applications: an overview.Genetic epidemiology · 2015Article
- Reproducible simulations of realistic samples for next-generation sequencing studies using Variant Simulation Tools.Genetic epidemiology · 2015Article
- The effects of demography and long-term selection on the accuracy of genomic prediction with sequence data.Genetics · 2014Article
- A C++ template library for efficient forward-time population genetic simulation of large populations.Genetics · 2014Article
- SMARTPOP: inferring the impact of social dynamics on genetic diversity through high speed simulations.BMC bioinformatics · 2014Article
- Genome evolution by matrix algorithms: cellular automata approach to population genetics.Genome biology and evolution · 2014Article
- forqs: forward-in-time simulation of recombination, quantitative traits and selection.Bioinformatics (Oxford, England) · 2014Article
- Article
- Ridge regression in prediction problems: automatic choice of the ridge parameter.Genetic epidemiology · 2013Article
- SLiM: simulating evolution with selection and linkage.Genetics · 2013Article
- Rapid forward-in-time simulation at the chromosome and genome level.BMC bioinformatics · 2013Article
- Properties and modeling of GWAS when complex disease risk is due to non-complementing, deleterious mutations in genes of large effect.PLoS genetics · 2013Article
- Poor Man's 1000 Genome Project: Recent Human Population Expansion Confounds the Detection of Disease Alleles in 7,098 Complete Mitochondrial Genomes.Frontiers in genetics · 2013Article
- On the structural plasticity of the human genome: chromosomal inversions revisited.Current genomics · 2012Article
- Simulated data for genomic selection and genome-wide association studies using a combination of coalescent and gene drop methods.G3 (Bethesda, Md.) · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
backgroundFREGENE simulates sequence-level data over large genomic regions in large populations. Because, unlike coalescent simulators, it works forwards through time, it allows complex scenarios of selection, demography, and recombination to be modelled simultaneously. Detailed tracking of sites under selection is implemented in FREGENE and provides the opportunity to test theoretical predictions and gain new insights into mechanisms of selection. We describe here main functionalities of both FREGENE and SAMPLE, a companion program that can replicate association study datasets.
resultsWe report detailed analyses of six large simulated datasets that we have made publicly available. Three demographic scenarios are modelled: one panmictic, one substructured with migration, and one complex scenario that mimics the principle features of genetic variation in major worldwide human populations. For each scenario there is one neutral simulation, and one with a complex pattern of selection.
conclusionFREGENE and the simulated datasets will be valuable for assessing the validity of models for selection, demography and population genetic parameters, as well as the efficacy of association studies. Its principle advantages are modelling flexibility and computational efficiency. It is open source and object-oriented. As such, it can be customised and the range of models extended.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.