Table 2.
Comparison of performances of several methods based on 55 alignments in HOM tests
| Method | Dataset | Accuracy (%) | Improvement | CPU time (s) |
|---|---|---|---|---|
| G-INS-i | ||||
| HOM+0 | 42.58b | — | 44.31 | |
| HOM+20 | 52.06 | +9.48c | 182.3 | |
| HOM+50 | 53.85 | +11.2c | 514.2 | |
| HOM+100 | 54.61 | +12.0c | 1405 | |
| H-INS-i | ||||
| HOM+0 | 43.20b | — | 38.68 | |
| HOM+20 | 49.56 | +6.36c | 151.2 | |
| HOM+50 | 53.37 | +10.2c | 426.8 | |
| HOM+100 | 53.29 | +10.1c | 1110 | |
| F-INS-i | ||||
| HOM+0 | 43.14b | — | 32.06 | |
| HOM+20 | 51.26 | +8.12c | 122.0 | |
| HOM+50 | 53.72 | +10.6c | 342.0 | |
| HOM+100 | 53.57 | +10.4c | 758.4 | |
| H-INS-1 | ||||
| HOM+0 | 38.55a | — | 14.30 | |
| HOM+20 | 46.00a | +7.45c | 73.81 | |
| HOM+50 | 48.80a | +10.3c | 237.9 | |
| HOM+100 | 48.35a | +9.80c | 636.6 | |
| FFT-NS-i | ||||
| HOM+0 | 43.57b | — | 32.57 | |
| HOM+20 | 49.57b | +6.00c | 73.84 | |
| HOM+50 | 50.68b | +7.11c | 155.87 | |
| HOM+100 | 50.73b | +7.16c | 365.8 | |
| FFT-NS-2 | ||||
| HOM+0 | 35.94a | — | 6.22 | |
| HOM+20 | 45.06a | +9.12c | 15.23 | |
| HOM+50 | 44.42a | +8.48c | 26.46 | |
| HOM+100 | 43.61a | +7.67c | 43.46 | |
| PROBCONS 1.06 | ||||
| HOM+0 | 47.95 | — | 91.13 | |
| HOM+20 | 51.78 | +3.83d | 590.1 | |
| HOM+50 | 51.59 | +3.64d | 2237 | |
| HOM+100 | 51.81 | +3.86d | 7634 | |
| MUSCLE-i 3.41 | ||||
| HOM+0 | 43.44b | — | 37.20 | |
| HOM+20 | 45.94b | +2.50 | 113.6 | |
| HOM+50 | 46.90a | +3.46 | 403.7 | |
| HOM+100 | 48.07a | +4.63c | 719.4 | |
| TCoffee 2.02 | ||||
| HOM+0 | 43.49b | — | 486.4 | |
| HOM+20 | 48.26 | +4.77c | 5007 | |
| HOM+50 | 49.71 | +6.22c | 28 250 | |
| HOM+100 | 49.94 | +6.45c | 71 390 | |
| CLUSTAL W 1.83 | ||||
| HOM+0 | 36.77a | — | 16.29 | |
| HOM+20 | 36.57a | –0.20 | 87.98 | |
| HOM+50 | 37.33a | +0.56 | 242.5 | |
| HOM+100 | 36.77a | +0.00 | 620.6 | |
The highest accuracy value within each dataset is in boldface.
aThe difference from the highest accuracy was shown to be significant (P < 0.01) by both the Wilcoxon test and the Friedman test.
bThe Wilcoxon test showed a significant difference but the Friedman test did not.
cThe improvement of score from HOM+0 was shown to be significant by both the Wilcoxon test and the Friedman test.
dThe Wilcoxon test showed a significant improvement but the Friedman test did not. See Table 1 for command-line options for each method in MAFFT. Command-line option for MUSCLE-i is muscle -maxiters 1000.