Skip to main content

Table 1 BRAliBase Cline scores

From: ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach

APSI [25%-100%] (N = 2,218)
Aligner Initial (I) Reformed (R) Avg. Dif. (R-I) p-value R > I R = I R < I
ClustalW 84.97% 86.09% 1.12% p < 0.001*** 40.22% 46.71% 13.07%
ClustalO 85.41% 87.71% 2.30% p < 0.001*** 44.00% 40.76% 15.24%
Kalign 89.30% 89.61% 0.30% p < 0.001*** 36.29% 46.93% 16.77%
Mafft (FFTnsi) 89.16% 89.94% 0.78% p < 0.001*** 27.23% 57.35% 15.42%
Mafft (Linsi) 88.63% 89.33% 0.70% p < 0.001*** 27.46% 55.91% 16.64%
Muscle 89.68% 89.89% 0.21% p < 0.001*** 21.51% 63.53% 14.97%
DialignTX 81.17% 84.82% 3.65% p < 0.001*** 54.78% 35.21% 10.01%
GramAlign 80.47% 84.90% 4.43% p < 0.001*** 54.64% 37.29% 8.07%
ProbCons 91.35% 91.34% −0.01% p = 0.127 27.41% 42.34% 30.25%
PicXAA 91.51% 91.46% −0.06% p < 0.001*** 26.28% 41.88% 31.83%
R-Coffee 91.34% 91.42% 0.08% p < 0.001*** 39.18% 32.33% 28.49%
APSI [25%-55%] (N = 869)
Aligner Initial (I) Reformed (R) Avg. Dif. (R-I) p-value R > I R = I R < I
ClustalW 69.03% 71.57% 2.54% p < 0.001*** 71.00% 14.04% 14.96%
ClustalO 69.19% 74.82% 5.63% p < 0.001*** 79.29% 3.68% 17.03%
Kalign 79.32% 79.95% 0.63% p < 0.001*** 53.28% 22.09% 24.63%
Mafft (FFTnsi) 78.46% 80.35% 1.89% p < 0.001*** 53.51% 23.82% 22.67%
Mafft (Linsi) 77.79% 79.38% 1.59% p < 0.001*** 48.10% 26.12% 25.78%
Muscle 79.79% 80.33% 0.54% p < 0.001*** 42.58% 34.52% 22.90%
DialignTX 59.75% 68.31% 8.56% p < 0.001*** 90.33% 0.69% 8.98%
GramAlign 66.63% 70.10% 3.47% p < 0.001*** 78.02% 11.85% 10.13%
ProbCons 83.39% 83.39% 0.00% p = 0.581 42.58% 10.01% 47.41%
PicXAA 83.77% 83.67% −0.10% p = 0.001*** 40.05% 9.21% 50.75%
R-Coffee 83.67% 83.57% −0.10% p = 0.429 46.49% 4.83% 48.68%
APSI [55%-75%] (N = 284)
Aligner Initial (I) Reformed (R) Avg. Dif. (R-I) p-value R > I R = I R < I
ClustalW 84.78% 85.40% 0.62% p < 0.001*** 48.94% 25.35% 25.70%
ClustalO 87.53% 87.91% 0.38% p = 0.001*** 49.30% 11.62% 39.08%
Kalign 86.37% 86.76% 0.39% p < 0.001*** 55.28% 25.35% 19.37%
Mafft (FFTnsi) 87.46% 87.76% 0.30% p = 0.004** 34.51% 37.32% 28.17%
Mafft (Linsi) 86.65% 86.80% 0.15% p = 0.875 28.87% 39.08% 32.04%
Muscle 87.80% 87.80% 0.00% p = 0.905 25.35% 46.48% 28.17%
DialignTX 83.49% 85.25% 1.76% p < 0.001*** 73.59% 5.63% 20.77%
GramAlign 81.75% 83.78% 2.03% p < 0.001*** 73.94% 17.25% 8.80%
ProbCons 89.23% 89.26% 0.03% p = 0.686 41.20% 19.72% 39.08%
PicXAA 89.34% 89.33% −0.01% p = 0.609 39.08% 21.83% 39.08%
R-Coffee 89.49% 89.59% 0.10% p = 0.014* 48.94% 11.27% 39.79%
APSI [75%-90%] (N = 840)
Aligner Initial (I) Reformed (R) Avg. Dif. (R-I) p-value R > I R = I R < I
ClustalW 98.16% 98.26% 0.10% p < 0.001*** 12.02% 81.79% 6.19%
ClustalO 98.20% 98.30% 0.10% p < 0.001*** 13.69% 80.36% 5.95%
Kalign 98.40% 98.41% 0.01% p = 0.074 13.21% 77.62% 9.17%
Mafft (FFTnsi) 98.52% 98.51% −0.01% p = 0.178 3.93% 90.95% 5.12%
Mafft (Linsi) 98.08% 98.23% 0.15% p < 0.001*** 10.83% 85.60% 3.57%
Muscle 98.41% 98.41% 0.00% p = 0.489 3.57% 92.38% 4.05%
DialignTX 98.15% 98.30% 0.15% p < 0.001*** 20.24% 72.86% 6.90%
GramAlign 92.78% 97.35% 4.57% p < 0.001*** 27.14% 66.07% 6.79%
ProbCons 98.61% 98.57% −0.04% p < 0.001*** 8.33% 78.81% 12.86%
PicXAA 98.61% 98.58% −0.03% p < 0.001*** 8.93% 77.62% 13.45%
R-Coffee 98.27% 98.48% 0.21% p < 0.001*** 27.74% 64.52% 7.74%
APSI [95%-100%] (N = 225)
Aligner Initial (I) Reformed (R) Avg. Dif. (R-I) p-value R > I R = I R < I
ClustalW 97.53% 97.59% 0.06% p = 0.030* 15.56% 68.89% 15.56%
ClustalO 97.62% 97.66% 0.04% p = 0.245 14.22% 72.89% 12.89%
Kalign 97.57% 97.63% 0.06% p < 0.001*** 32.89% 55.56% 11.56%
Mafft (FFTnsi) 97.72% 97.70% −0.02% p = 0.009** 3.56% 86.67% 9.78%
Mafft (Linsi) 97.67% 97.73% 0.06% p = 0.642 8.00% 81.33% 10.67%
Muscle 97.68% 97.67% −0.01% p = 0.011* 2.22% 89.33% 8.44%
DialignTX 97.58% 97.69% 0.11% p < 0.001*** 22.67% 65.33% 12.00%
GramAlign 86.28% 96.95% 10.67% p < 0.001*** 42.67% 53.33% 4.00%
ProbCons 97.66% 97.67% 0.01% p = 0.299 22.67% 59.56% 17.78%
PicXAA 97.67% 97.68% 0.01% p = 0.526 21.78% 60.00% 18.22%
R-Coffee 97.41% 97.68% 0.27% p < 0.001*** 41.33% 44.89% 13.78%
  1. Cline scores corresponding to the 2,218 alignments of the BRAliBase dataset. *significant at p<0.05, **significant at p<0.005, ***significant at p≤0.001. The first sub-table summarizes the performance of each alignment pair averaged over all test cases whereas the remaining sub-tables report the results organized according to the average pairwise sequence identity of the sequences. For every sub-table, the APSI value and the number of alignments (N) corresponding to each group are reported in the first row. Columns 2 and 3 correspond to the average Cline scores of the initial (I) and the reformed (R) alignments respectively. The average differences (R-I) per alignment pair are given in the fourth column and the corresponding p-values of these differences are given at the fifth column (statistically significant values at the .05 significance level are highlighted in bold). Finally, columns 6–8 indicate the percentage of cases where the reformed alignments were superior, equal or inferior (in terms of Cline score) to the initial alignment.