TABLE B2

Performance for models with uniform recombination rates with phased data for some additional parameters [n = 50, L = 125 bp, 50-kb sequences with θ = 40.0, grid (0, 2, 4, 6, 8, … , 50)]

γaρag(γ)bg(ρ)bB(γ)cB(ρ)cE()dE()dV(γ)eV(ρ)e
Hudson's composite-likelihood method
12120.1720.9150.6180.53514.6612.281.6160.459
1680.2060.8840.5920.55317.358.241.2610.570
Summary statistics method
12120.3280.8950.4840.51118.0512.621.4990.505
1680.4040.8570.4780.52820.288.501.0830.595
• a γ and ρ denote the true values of the gene-conversion and crossing-over rates under which 1000 data sets were simulated.

• b g(γ) and g(ρ) denote the fraction of the data sets for which the estimates of gene conversion () and crossing over () lie within a factor of 2 of the true values (i.e., γ and ρ), respectively.

• c B(γ) and B(ρ) denote the fraction of times the estimates of gene conversion and crossing over are lower than the true values, given that they are not equal to the true values.

• d E() and E() denote the mean of the estimates of gene-conversion and crossing-over rates.

• e V(γ) and V(ρ) denote the root mean square relative error for the estimates.