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

BMC Bioinformatics

Table 4 Validation results by sequenceLDhot for 2- and 5-hotspot models (20 replicates each) (genomic sequence length = 0.2-Mb)

Number of hotspots	Simulator	# Detected peaks/Total # simulated peaks	Mean (standard deviation) of LR	Mean shifting (kb)^*	# Significant shiftings^†/# Detected peaks
2	msHOT	39/40	45.83 (18.35)	-26	2/39
	MaCS	38/40	28.73 (23.36)	86.65	4/38
	fastsimcoal	36/40	41.16 (20.75)	10.8	2/36
5	msHOT	91/100	47.49 (28.87)	-981.33	13/91
5	MaCS	93/100	43.32 (25.48)	-57	11/93
	fastsimcoal	94/100	48.78 (22.06)	-35	14/94

*A negative number indicates a shifting to the left of the expected position.
^†A significant shifting was defined as a shifting out of the range defined by ± 1-kb away from the expected peak position.

ISSN: 1471-2105