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
|
||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| M2
|
M2a
|
M8
|
M1 vs. M2a
|
M1a vs. M2aa
|
M7 vs. M8a
|
M8a vs. M8a
|
M8a vs. M8 (1 d.f.)a |
|||||||||||
| Simulation scheme |
Topology | Prob: | >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) |
A | 0.05 | 0.05 | 0.33 | 0.30 | 0.24 | 0.23 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.03 | 0.08 | 0.08 | 0.03 | 0.03 | |
| B | 0.14 | 0.14 | 0.28 | 0.26 | 0.29 | 0.29 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.01 | ||
| Scheme 2a (50% ω = 0, 50% ω = 1) |
A | 0.12 | 0.12 | 0.14 | 0.14 | 0.08 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | |
| B | 0.12 | 0.11 | 0.13 | 0.12 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | ||
| Scheme 2b (90% ω = 0, 10% ω = 1) |
A | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | |
| B | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | ||
| Scheme 3 (50% ω = 0.5, 50% ω = 1) |
A | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | |
| B | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | ||
a
LRT test between the two models at significance level of 0.05.