Table 2. A comparison of the performance of different tree inference methods following realignment of simulated sequences.
| Realignmnet FFT-NS-1 | RFd | FP | FN | Precision | Recall | |||||
| PhyML 4G SPR (SH 50) (3) | 58.3 | a | 19.3 | a | 39.0 | a | 0.912 | a | 0.843 | a |
| RAxML (3) | 61.2 | a | 30.6 | b | 30.6 | a | 0.877 | b | 0.877 | a |
| PhyML 4G SPR (3) | 63.5 | a | 31.8 | b | 31.8 | a | 0.872 | b | 0.872 | a |
| PhyML 4G (SH50) (3) | 75.4 | a | 26.7 | b | 48.7 | a | 0.877 | b | 0.804 | a |
| FastTree (SH50) (3) | 77.8 | a | 31.6 | b | 46.2 | a | 0.861 | b | 0.814 | a |
| PhyML 1G (SH50) (3) | 82.2 | a | 30.8 | b | 51.5 | a | 0.861 | b | 0.792 | a |
| FastTree (3) | 82.6 | a | 41.3 | c | 41.4 | a | 0.833 | c | 0.833 | a |
| PhyML 4G (3) | 83.4 | a | 41.7 | c | 41.7 | a | 0.832 | c | 0.832 | a |
| PhyML 1G (3) | 89.2 | a | 44.6 | c | 44.6 | a | 0.820 | c | 0.820 | a |
| DendroBLAST (1) | 95.1 | 27.6 | 67.5 | 0.867 | 0.732 | |||||
| FastME SPR (2) | 112.4 | c | 56.2 | c | 56.2 | a | 0.773 | c | 0.773 | a |
| FastME (2) | 116.1 | c | 58.1 | c | 58.1 | a | 0.766 | c | 0.766 | a |
| QuickTree log cor. (2) | 119.4 | c | 59.7 | c | 59.7 | a | 0.759 | c | 0.759 | a |
| QuickTree (con50) (2) | 149.3 | c | 70.5 | c | 78.8 | c | 0.702 | c | 0.682 | c |
| QuickTree (2) | 157.5 | c | 78.8 | c | 78.8 | c | 0.682 | c | 0.682 | c |
Please refer to the legend for table 1 for explanations of abbreviations.