Table 1.

Summarized description of the simulated datasets used for experimental evaluation (see Supplementary Data 1 for command lines)

Dataset #	Sweep type	Confounding factor	Simulation software	Varying parameters	Range of values
	Hard, complete	Bottleneck	Hudson’s ms and mssel	Severity (−eN)	0.005–0.5
1–60				Duration (−eN)	80–400 (4N0 generations)
				Beginning (−eN)	800–20,000 (4N0 generations)
61–70	Hard, complete	Migration	Hudson’s ms and mssel	Population join (−ej)	0.003–3 (4N0 generations)
71–80	Soft, complete	None	Discoal	Drift until frequency (-f)	0.1–1.0
81–101	No sweep	Recombination	msHOT	Hotspot region size (−v) Hotspot intensity (−v)	5–10 kb 2–100
102–111	Hard, complete	Recombination	msHOT and mbs	Hotspot region size (−v) Hotspot intensity (−v)	5 kb 2–20
112–113	Hard, complete	Background selection	SFS_CODE	a) Set of SNPs with demography b) Set of SNPs with demography + background selection c) Set of SNPs with demography + background selection + sweep