Table 2.

Performance of Hudson’s Pairwise Composite Likelihood Method

A. Data Simulated with Uniform Crossing Over and Uniform Conversion
Rate
ρ	γ	a	g(γ)b	B(γ)c	a	g(ρ)b	B(ρ)c
20	40	38.02	.25	.64	20.78	.80	.55
40	40	33.82	.21	.71	44.22	.84	.49
60	40	42.10	.21	.68	64.10	.85	.48
30	20	29.82	.13	.66	31.84	.82	.53
30	40	38.08	.25	.67	31.63	.84	.51
30	60	44.82	.28	.72	33.07	.81	.49
B. Data Simulated with Nonuniform Crossing Over and Uniform Conversion
Rate
ρ	γ	a	g(γ)b	B(γ)c	a	g(ρ)b	B(ρ)c
20	40	29.01	.26	.73	21.05	.81	.54
40	40	23.06	.14	.81	40.71	.83	.56
60	40	18.43	.17	.85	58.60	.90	.58
30	20	14.95	.12	.78	29.17	.83	.59
30	40	22.55	.21	.80	30.85	.82	.54
30	60	36.45	.28	.77	30.94	.83	.55

^a and denote the averages of the MLEs of gene-conversion () and crossing-over () rates for the 500 data sets simulated at the corresponding crossing-over (ρ) and gene-conversion (γ) rate.

^bg(γ) and g(ρ) denote the fraction of times and for a simulated data set is within a factor of 2 of the true γ and ρ, respectively (Wall 2000).

^cB(γ) and B(ρ)denote the fraction of times and are less than their true values.