One long branch |
---|
 |
No model violation
1
|
Model violation
1
|
 | First2 | Wrong | Burd SD | Mean SD | Burd ED | Mean ED | First | Wrong | Burd SD | Mean SD | Burd ED | Mean ED |
ML3 | 30 | 56 | 144 | 2.57 | 56 | 1.00 | 20 | 65 | 164 | 2.52 | 65 | 1.00 |
BUU | 30 | 46 | 232 | 5.04 | 46 | 1.00 | 20 | 50 | 222 | 4.44 | 50 | 1.00 |
BGU | 30 | 36 | 96 | 2.67 | 36 | 1.00 | 20 | 39 | 118 | 3.03 | 39 | 1.00 |
BGE | 30 | 28 | 88 | 3.14 | 28 | 1.00 | 20 | 39 | 116 | 2.97 | 39 | 1.00 |
Two long branches
|
 |
No model violation
|
Model violation
|
 | First | Wrong | Burd SD | Mean SD | Burd ED | Mean ED | First | Wrong | Burd SD | Mean SD | Burd ED | Mean ED |
ML | 20 | 186 | 1124 | 6.04 | 273 | 1.47 | 20 | 174 | 1166 | 6.70 | 207 | 1.19 |
BUU | 20 | 237 | 1854 | 7.82 | 326 | 1.38 | 10 | 244 | 1900 | 7.79 | 299 | 1.23 |
BGU | 20 | 87 | 270 | 3.10 | 104 | 1.20 | 20 | 105 | 468 | 4.46 | 119 | 1.13 |
BGE | 20 | 86 | 314 | 3.65 | 101 | 1.17 | 20 | 115 | 650 | 5.65 | 131 | 1.14 |
- 1 Protein-sequence data were evolved under the Jones et al. (JTT) or, alternatively, mammalian mitochondrial (mtmam) model of sequence change, and trees were inferred assuming the JTT model.
- 2 Performance was measured by six indices: First, the lowest investigated branch-length ratio at which at least one inaccurately reconstructed tree was found; Wrong, the number of inaccurately inferred trees out 400 (8 branch-length ratios × 50 replicates at each ratio); BurdSD, the bipartition burden, calculated as the Robinson-Foulds symmetric distance by which each tree differs from the known tree, summed over the 400 trees; MeanSD, the mean Robinson-Foulds symmetric distance per inaccurate tree; BurdED, the edit burden, calculated as the edit distance by which each tree differs from the known tree, summed over the 400 trees; and MeanED, the mean edit distance per inaccurate tree.
- 3 Inference methods: ML, protein maximum likelihood with gamma ASRV correction; BUU, Bayesian inference, uncorrected for ASRV, uniform prior; BGU, Bayesian inference, gamma ASRV correction, uniform prior; and BGE, Bayesian inference, gamma ASRV correction, exponential prior. See text for further details.