Table 4.

Forward Simulators for Genomic Data Under Different Evolutionary and Demographic Scenarios

Simulator	Vrec	Sel	Vmu	Gconv	Mig	HS	Vdm	DisM	GD	EF	Phen	Reference
simuPOP	Yes	Yes	Yes	No	Yes	No	Yes	Yes	Yes	No	Yes	(Peng and Kimmel, 2005)
genomeSIM	Yes	No	No	No	No	No	No	Yes	No	No	Yes	(Dudek et al., 2006)
Nemo	Yes	Yes	Yes	No	Yes	No	Yes	No	No	Yes	Yes	(Guillaume and Rougemont, 2006)
FREGENE	Yes	Yes	No	Yes	Yes	Yes	Yes	Yes	No	No	Yes	(Hoggart et al., 2007)
GenomePop	Yes	Yes	Yes	No	Yes	Yes	Yes	No	Yes	No	No	(Carvajal-Rodriguez, 2008)
genomeSIMLA	Yes	No	No	No	Yes	Yes	No	Yes	Yes	Yes	Yes	(Edward et al., 2008)
SFS_CODE	No	Yes	Yes	Yes	Yes	Yes	Yes	No	No	No	No	(Hernandez, 2008)
ForSim	No	Yes	No	No	Yes	No	Yes	Yes	Yes	Yes	Yes	(Lambert et al., 2008)
QuantiNEMO	Yes	Yes	No	No	Yes	No	Yes	Yes	Yes	Yes	Yes	(Neuenschwander et al., 2008)
ForwSim	Yes	Yes	No	No	No	No	No	No	Yes	No	No	(Padhukasahasram et al., 2008)

Note that all the above listed simulators allow for recombination. “Yes” or “No” indicates whether the simulator incorporates a given modeling capability. Vrec, variable recombination rates; Sel, selection; Vmu, various mutation models; GConv, gene conversion; Mig, migration; HS, recombination, mutation, or gene conversion hotspots; Vdm, various demographic models; DisM, various disease models; GD, genetic drift; EF, environmental factors; Phen, generates phenotypes (i.e., quantitative or binary [case-control] traits).