Table 1.
Sum-of-pairs scores of various alignment programs on the benchmark database IRMBASE 2
| Method (Protein) | REF1 | REF2 | REF3 | REF4 | Total |
| DIALIGN-TX | 89.42 | 94.90 | 93.75 | 93.64 | 92.93 |
| DIALIGN-T 0.2.2 | 89.670 | 94.190 | 93.930 | 93.120 | 92.730 |
| DIALIGN 2.2 | 90.430 | 93.40- | 91.78-- | 92.98- | 92.15-- |
| CLUSTAL W2 | 07.13-- | 10.63-- | 19.87-- | 26.17-- | 15.95-- |
| T-COFFEE 5.56 | 72.67-- | 77.80-- | 83.03-- | 83.48- | 79.24-- |
| POA V2 | 87.56- | 49.57-- | 41.90-- | 37.56-- | 54.15-- |
| MAFFT 6.240 L-INSi | 82.780 | 84.29- | 84.15-- | 82.42-- | 84.41-- |
| MAFFT 6.240 E-INSi | 90.530 | 94.370 | 93.110 | 94.79+ | 93.20+ |
| MUSCLE 3.7 | 32.67-- | 34.82-- | 54.19-- | 57.84-- | 44.88-- |
| PROBCONS 1.12 | 78.78-- | 86.82-- | 87.29- | 87.69-- | 85.15-- |
Average sum-of-pair scores (SPS) of the benchmarked programs on the core blocks (given by the implanted conserved motifs) of IRMBASE 2. Minus symbols denote statistically significant inferiority of the respective method compared with DIALIGN-TX, while plus symbols denote statistically significant superiority of the method. 0 denotes non-significant superiority or inferiority of DIALIGN-TX, respectively. Single plus or minus symbols denote significance according to the Wilcoxon Matched Pairs Signed Rank Test with p ≤ 0.05 and double symbols denote significance with p ≤ 0.001, respectively.