Table 4.
The column (CS) and sum-of-pair (Q) scores of the BAliBASE test cases in references 1–5
| Method | REF 1 (82) (%) | P | REF 2 (23) (%) | P | REF 3 (12) (%) | P | REF 4 (12) (%) | P | REF 5 (12) (%) | P | Weighted average (%) | P |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Column scores (CS) | ||||||||||||
| PRALINEBASIC | 76.9 | 0.425 | 51.0 | 0.593 | 54.0 | 0.786 | 38.5 | 0.991 | 59.8 | 0.786 | 66.0 | 0.187 |
| PRALINEPREPRO | 78.4 | 0.425 | 56.2 | 0.842 | 50.8 | 0.786 | 30.7 | 0.991 | 77.1 | 0.786 | 68.3 | 0.949 |
| PRALINEPSI | 83.9 | – | 61.0 | – | 55.8 | – | 53.9 | – | 68.6 | – | 73.9 | – |
| T-COFFEEv2.03 | 78.9 | 0.548 | 58.5 | 0.593 | 54.8 | 0.786 | 70.8 | 0.186 | 86.1 | 0.186 | 73.4 | 0.768 |
| MUSCLEv3.51 | 79.9 | 0.914 | 60.2 | 0.842 | 58.3 | 0.786 | 63.3 | 0.186 | 91.4 | 0.066 | 74.4 | 0.858 |
| Sum-of-pairs scores (Q) | ||||||||||||
| PRALINEBASIC | 85.0 | 0.319 | 91.0 | 0.017 | 77.1 | 0.991 | 73.2 | 0.991 | 82.5 | 0.786 | 84.1 | 0.030 |
| PRALINEPREPRO | 86.0 | 0.425 | 93.1 | 0.593 | 77.9 | 0.991 | 74.1 | 0.991 | 88.9 | 0.991 | 85.7 | 0.858 |
| PRALINEPSI | 90.4 | – | 94.0 | – | 76.4 | – | 79.9 | – | 81.8 | – | 88.2 | – |
| T-COFFEEv2.03 | 86.2 | 0.425 | 93.9 | 0.842 | 76.7 | 0.786 | 88.3 | 0.433 | 94.6 | 0.186 | 87.5 | 0.858 |
| MUSCLEv3.51 | 87.0 | 0.914 | 93.7 | 0.842 | 79.6 | 0.433 | 88.9 | 0.186 | 97.8 | 0.019 | 88.5 | 0.928 |
The scores are listed separately for each reference set and the overall average, weighted relative to the number of alignments in each reference set (numbers in parentheses are the number of alignments each set contains). The ‘P’ columns show the statistical significance (P-value from Kolmogorov–Smirnov test) of the results of each method compared with PRALINEPSI. P-values below 0.05 are underlined.