Table 3. A comparison of the performance of different tree inference methods following trimming of realigned simulated sequences.
| GBLOCKS trimmed FFT-NS-1 | RFd | FP | FN | Precision | Recall | |||||
| PhyML 4G SPR (SH 50) (3) | 68.4 | a | 21.8 | a | 46.5 | a | 0.896 | a | 0.813 | a |
| RAxML (3) | 74.1 | a | 37.0 | c | 37.0 | a | 0.851 | b | 0.851 | a |
| PhyML 4G SPR (3) | 76.3 | a | 38.1 | c | 38.1 | a | 0.847 | c | 0.847 | a |
| PhyML 4G (SH50) (3) | 82.1 | a | 27.4 | b | 54.7 | a | 0.868 | b | 0.780 | a |
| FastTree (SH50) (3) | 86.9 | a | 35.4 | c | 51.5 | a | 0.843 | b | 0.793 | a |
| PhyML 4G (3) | 87.1 | a | 30.9 | c | 56.2 | a | 0.855 | c | 0.775 | a |
| FastTree (3) | 92.2 | a | 46.0 | c | 46.2 | a | 0.814 | c | 0.814 | a |
| PhyML 1G (SH50) (3) | 93.1 | a | 46.6 | c | 46.5 | a | 0.814 | c | 0.811 | a |
| DendroBLAST (1) | 95.1 | 27.6 | 67.5 | 0.867 | 0.732 | |||||
| PhyML 1G (3) | 96.5 | b | 48.2 | c | 48.2 | a | 0.806 | c | 0.806 | a |
| FastME SPR (2) | 119.5 | c | 59.8 | c | 59.8 | a | 0.759 | c | 0.759 | a |
| FastME (2) | 123.7 | c | 61.9 | c | 61.9 | a | 0.751 | c | 0.751 | a |
| QuickTree log cor. (2) | 124.0 | c | 62.0 | c | 62.0 | a | 0.748 | c | 0.748 | c |
| QuickTree (con50) (2) | 128.3 | c | 28.8 | b | 99.5 | c | 0.834 | c | 0.599 | c |
| QuickTree (2) | 161.6 | c | 80.9 | c | 80.9 | c | 0.674 | c | 0.674 | c |
Please refer to the legend for table 1 for explanations of abbreviations.