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SelSim specifications

Information


Unique identifier OMICS_07253
Name SelSim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Advanced
Version 2.1
Stability No
Maintained No

Versioning


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Publication for SelSim

SelSim citations

 (11)
library_books

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

2014
BMC Bioinformatics
PMCID: 3890628
PMID: 24387001
DOI: 10.1186/1471-2105-15-3

[…] pe block patterns delineated by recombination hotspots along chromosomes in fine-mapping locations of disease loci. Over the past decade, a plethora of coalescent simulators have been developed, e.g. SelSim [], CoaSim [], FastCoal [], Mlcoalsim [], and RECOAL [], to name a few. Of them, five most representative and widely used coalescent simulators, Hudson’s ms [], msHOT [], Markovian Coalescent S […]

library_books

Inferring Selection Intensity and Allele Age from Multilocus Haplotype Structure

2013
PMCID: 3737182
PMID: 23797107
DOI: 10.1534/g3.113.006197

[…] Using the coalescent simulator SelSim (), data are generated for two sets of parameters corresponding to medium and strong selection respectively: θ = 4Nμ = 500, ρ = 4Nr = 500, Ns = 50, and θ = 4Nμ = 500, ρ = 4Nr = 500, Ns = 500, w […]

call_split

No Evidence for Strong Recent Positive Selection Favoring the 7 Repeat Allele of VNTR in the DRD4 Gene

2011
PLoS One
PMCID: 3164202
PMID: 21909391
DOI: 10.1371/journal.pone.0024410
call_split See protocol

[…] Using SelSim program based on the coalescent theory, 120 chromosomes bearing 101 SNPs evenly distributed in the region with the size of 1 cM were simulated assuming a population with constant size, N, of 5 […]

call_split

Scanning for Genomic Regions Subject to Selective Sweeps Using SNP MaP Strategy

2011
PMCID: 5054161
PMID: 21382594
DOI: 10.1016/S1672-0229(10)60027-7
call_split See protocol

[…] To obtain genomic regions under selective sweeps, coalescent simulations were performed using the program SelSim . We assumed that the advantageous mutation follows a stochastic trajectory, and set the strength of selection as the population selection coefficient (δ=2Nes=0, 20, 100, and 200). Other parame […]

call_split

Haplotype allelic classes for detecting ongoing positive selection

2010
BMC Bioinformatics
PMCID: 2831848
PMID: 20109229
DOI: 10.1186/1471-2105-11-65
call_split See protocol

[…] s to Ne = 1,000 in the last 300 generations (see Additional File ). Recombination was tested under the standard scenario with a population recombination rate ρ = Θ/2, kept constant along the sequence.SelSim [] was used to simulate sets of replicates under an ongoing selective sweep. In a default selection scenario, a population evolves under the standard scenario with the evaluated SNP brought to […]

library_books

Detecting natural selection by empirical comparison to random regions of the genome

2009
Hum Mol Genet
PMCID: 2778377
PMID: 19783549
DOI: 10.1093/hmg/ddp457

[…] The simulations of selection were carried out with SelSim (). Each simulated sample contained 100 haplotypes with a length of 30 kb, meant to approximately match the settings of our real data. We assumed a constant recombination rate of 1.25 cM/Mb and […]

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SelSim institution(s)
Department of Statistics, Oxford, UK

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