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Table 2 DNA SMART Cline scores

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

APSI [25%-90%] (N = 264)
Aligner Initial (I) Reformed (R) Avg. Dif. (R-I) p-value R > I R = I R < I
ClustalW 59.55% 67.06% 7.51% p < 0.001*** 95.08% 0.76% 4.17%
ClustalO 70.94% 74.25% 3.31% p < 0.001*** 74.24% 3.79% 21.97%
Kalign 68.37% 72.37% 4.00% p < 0.001*** 87.50% 3.41% 9.09%
Mafft (FFTnsi) 71.93% 74.81% 2.88% p < 0.001*** 60.98% 3.79% 35.23%
Mafft (Linsi) 79.70% 78.26% −1.44% p < 0.001*** 33.71% 7.20% 59.09%
Muscle 69.51% 72.52% 3.01% p < 0.001*** 70.08% 3.79% 26.14%
DialignTX 60.82% 70.13% 9.31% p < 0.001*** 87.50% 1.52% 10.98%
GramAlign 66.96% 70.11% 3.15% p < 0.001*** 74.62% 4.17% 21.21%
ProbCons 73.68% 73.90% 0.22% p = 0.099 54.55% 3.41% 42.05%
PicXAA 75.64% 73.85% −1.79% p < 0.001*** 28.03% 3.03% 68.94%
  1. Cline scores corresponding to the 264 alignments of the DNA SMART dataset. *significant at p<0.05, **significant at p<0.005, ***significant at p≤0.001. The average Cline scores corresponding to the initial (I) and the reformed (R) alignments are given at columns 2 and 3 respectively. Column 4 represents the differences of the Cline Scores (R-I) per alignment pair and the statistical significance of these differences is given at column 5 (statistically significant values at the .05 significance level are highlighted in bold). The last three columns correspond to the percentage of cases where the reformed alignments were superior, equal or inferior (in terms of Cline score) to the initial alignment.