Table 1. Comparative performance of FEL and MEME on simulated data where varies along phylogenetic lineages.
Japanese encephalitis virus env | Vertebrate rhodopsin | Camelid VHH | ||||||||
ω− | q + | ω+ = 4 | ω+ = 12 | ω+ = 36 | ω+ = 4 | ω+ = 12 | ω+ = 36 | ω+ = 4 | ω+ = 12 | ω+ = 36 |
0 | 0.1 | 0.00 0.06 | 0.01 0.25 | 0.03 0.50 | 0.00 0.21 | 0.00 0.53 | 0.02 0.81 | 0.00 0.53 | 0.00 0.95 | 0.04 0.99 |
0 | 0.25 | 0.01 0.12 | 0.06 0.32 | 0.12 0.51 | 0.01 0.30 | 0.04 0.68 | 0.15 0.88 | 0.00 0.66 | 0.14 0.98 | 0.56 1.00 |
0 | 0.5 | 0.06 0.12 | 0.19 0.29 | 0.34 0.45 | 0.09 0.28 | 0.34 0.59 | 0.54 0.82 | 0.23 0.77 | 0.85 0.98 | 0.96 0.98 |
0.2 | 0.1 | 0.00 0.05 | 0.01 0.21 | 0.02 0.41 | 0.00 0.09 | 0.01 0.35 | 0.02 0.67 | 0.00 0.16 | 0.01 0.87 | 0.04 0.98 |
0.2 | 0.25 | 0.02 0.08 | 0.07 0.27 | 0.14 0.48 | 0.03 0.17 | 0.09 0.55 | 0.17 0.84 | 0.01 0.42 | 0.27 0.96 | 0.62 0.99 |
0.2 | 0.5 | 0.05 0.11 | 0.18 0.29 | 0.36 0.49 | 0.13 0.25 | 0.36 0.60 | 0.55 0.76 | 0.30 0.72 | 0.84 0.99 | 0.90 0.99 |
0.4 | 0.1 | 0.00 0.04 | 0.01 0.15 | 0.03 0.37 | 0.01 0.07 | 0.02 0.30 | 0.03 0.57 | 0.01 0.10 | 0.04 0.78 | 0.10 0.97 |
0.4 | 0.25 | 0.02 0.06 | 0.09 0.27 | 0.15 0.45 | 0.04 0.16 | 0.09 0.49 | 0.21 0.78 | 0.03 0.32 | 0.33 0.97 | 0.63 0.99 |
0.4 | 0.5 | 0.07 0.10 | 0.17 0.26 | 0.33 0.46 | 0.17 0.28 | 0.39 0.58 | 0.51 0.76 | 0.40 0.62 | 0.82 0.94 | 0.96 1.00 |
Power to detect sites under selection () are reported for FEL and MEME (in boldface) for each unique combination of negative selection (), positive selection (), and proportion of branches under positive selection () parameters.