TABLE 4

Proportion of false-positive predictions (number of sites that were wrongly categorized as positively selected divided by the total number of nonpositively selected sites) reported by codeml on simulated data with no positive selection

Proportion of false positives
M2M2aM8M1 vs. M2aM1a vs. M2aaM7 vs. M8aM8a vs. M8aM8a vs. M8
 (1 d.f.)a
Simulation
 schemeTopologyProb:>0.95>0.99>0.95>0.99>0.95>0.99>0.95>0.99>0.95>0.99>0.95>0.99>0.95>0.99>0.95>0.99
Scheme 1
   (100% ω = 1)A0.050.050.330.300.240.230.000.000.020.020.030.030.080.080.030.03
B0.140.140.280.260.290.290.000.000.000.000.000.000.020.020.010.01
Scheme 2a
   (50% ω = 0,
   50% ω = 1)A0.120.120.140.140.080.070.000.000.000.000.000.000.000.000.000.00
B0.120.110.130.120.020.020.000.000.000.000.000.000.000.000.000.00
Scheme 2b
   (90% ω = 0,
   10% ω = 1)A0.000.000.000.000.000.000.000.000.000.000.000.000.000.000.000.00
B0.010.010.000.000.030.030.000.000.000.000.000.000.000.000.000.00
Scheme 3
   (50% ω = 0.5,
   50% ω = 1)A0.000.000.000.000.000.000.000.000.000.000.000.000.000.000.000.00
B0.000.000.000.000.000.000.000.000.000.000.000.000.000.000.000.00
  • a LRT test between the two models at significance level of 0.05.