Simulation results in same-strand (SS) and opposite-strand (OP) overlaps.

Estimations of the ratios of nonsynonymous to synonymous rates in the two genes ( and ) by simultaneous estimation (blue line) and by independent estimation (red line) are plotted against the true value (X axis, dashed green line) for five types of overlap. The simulated value of was set to 0.2 and was varied between 0.2 and 2. k was set to 1 and t was set to 0.35. Each data point is the median of 100 replications. Vertical lines mark the lower and upper quartiles. Top: estimation of . Bottom: estimation of . Dotted black lines (X = 1 and Y = 1) illustrate the range of parameters that result in false inference of positive selection by independent estimation, i.e., when simulated and estimated .