Table 3.

Significance of differences in BAliBASE 3.0 SP/TC scores

Aligner		XX-XX RV11	XX-XX RV12	XX-XX RV20	XX-XX RV30	XX-XX RV40	XX-XX RV50	Total
Non-progressive methods
DIALIGN-T		$$\frac{+8.6e-8}{+1.5e-6}$$	$$\frac{+7.7e-9}{+2.2e-8}$$	$$\frac{+1.3e-7}{+9.6e-5}$$	$$\frac{+2.7e-6}{+0.0024}$$	$$\frac{+2.1e-9}{+4.9e-8}$$	$$\frac{+0.00098}{+0.027}$$	$$\frac{+5.3e-36}{+3.6e-26}$$
FSA		$$\frac{+8.6e-8}{+1.2e-6}$$	$$\frac{+3.5e-6}{+0.00012}$$	$$\frac{+3.6e-8}{+1.2e-6}$$	$$\frac{+2.6e-6}{+8.5e-6}$$	$$\frac{+8.3e-9}{+1.2e-6}$$	$$\frac{+0.00081}{+0.021}$$	$$\frac{+3.6e-34}{+3.5e-27}$$
PicXAA		$$\frac{+0.048}{+\left(0.53\right)}$$	$$\frac{-\left(0.82\right)}{-\left(0.98\right)}$$	$$\frac{-\left(0.055\right)}{-0.018}$$	$$\frac{-2.8e-5}{-7.2e-6}$$	$$\frac{+\left(0.11\right)}{-\left(0.052\right)}$$	$$\frac{-\left(0.063\right)}{-\left(0.37\right)}$$	$$\frac{-0.0079}{-1.3e-6}$$
Progressive methods
Clustal Ω		$$\frac{+2.6e-7}{+5.1e-5}$$	$$\frac{+2.4e-5}{+0.00019}$$	$$\frac{+0.0048}{-0.00054}$$	$$\frac{-0.020}{-0.00060}$$	$$\frac{+2.2e-6}{+\left(0.16\right)}$$	$$\frac{+0.017}{-\left(0.77\right)}$$	$$\frac{+1.1e-13}{+\left(0.30\right)}$$
DIALIGN-TX		$$\frac{+1.0e-7}{+1.3e-6}$$	$$\frac{+6.2e-8}{+4.0e-7}$$	$$\frac{+2.3e-7}{+0.00040}$$	$$\frac{+8.7e-6}{+0.038}$$	$$\frac{+2.8e-9}{+1.3e-7}$$	$$\frac{+0.0017}{+\left(0.066\right)}$$	$$\frac{+3.1e-34}{+9.5e-23}$$
MAFFT		$$\frac{+0.0031}{+\left(0.11\right)}$$	$$\frac{+0.00085}{+0.005}$$	$$\frac{-\left(0.64\right)}{-\left(0.052\right)}$$	$$\frac{-0.0009}{-0.0007}$$	$$\frac{+0.0005}{+\left(0.07\right)}$$	$$\frac{-\left(0.072\right)}{-\left(0.062\right)}$$	$$\frac{+0.028}{-\left(0.55\right)}$$
MSAProbs		$$\frac{+0.028}{+\left(0.23\right)}$$	$$\frac{-\left(0.90\right)}{-\left(0.67\right)}$$	$$\frac{-0.011}{-0.00032}$$	$$\frac{-0.00017}{-1.4e-5}$$	$$\frac{+\left(0.61\right)}{+0.048}$$	$$\frac{-0.010}{-0.0086}$$	$$\frac{-0.020}{-5.9e-8}$$
MUSCLE		$$\frac{+7.3e-6}{+0.00017}$$	$$\frac{+2.8e-6}{+0.00015}$$	$$\frac{+0.00015}{+\left(0.15\right)}$$	$$\frac{+\left(0.19\right)}{+\left(0.52\right)}$$	$$\frac{+7.6e-9}{+2.8e-6}$$	$$\frac{+0.010}{+\left(0.072\right)}$$	$$\frac{+2.9e-22}{+3.3e-12}$$
Probalign		$$\frac{+\left(0.67\right)}{+\left(0.52\right)}$$	$$\frac{-\left(0.63\right)}{-\left(0.88\right)}$$	$$\frac{-0.032}{-6.8e-5}$$	$$\frac{-0.0099}{-0.00056}$$	$$\frac{+\left(0.62\right)}{+\left(0.060\right)}$$	$$\frac{-\left(0.18\right)}{-\left(0.32\right)}$$	$$\frac{-0.019}{-6.0e-6}$$
ProbCons		$$\frac{+0.021}{+0.037}$$	$$\frac{+0.0042}{+\left(0.19\right)}$$	$$\frac{+0.028}{-\left(0.19\right)}$$	$$\frac{-\left(0.15\right)}{-0.010}$$	$$\frac{+0.00026}{+0.022}$$	$$\frac{-\left(0.12\right)}{-\left(0.17\right)}$$	$$\frac{+0.00087}{+\left(0.93\right)}$$
T-Coffee		$$\frac{+0.0024}{+0.016}$$	$$\frac{+0.0017}{+0.013}$$	$$\frac{+0.0075}{-\left(0.51\right)}$$	$$\frac{-\left(0.29\right)}{-\left(0.099\right)}$$	$$\frac{+9.7e-5}{+\left(0.29\right)}$$	$$\frac{-0.048}{-0.026}$$	$$\frac{+1.3e-5}{+\left(0.70\right)}$$

Entries show p-values indicating the significance of the mean difference of SP/TC scores between MSARC and other aligners as measured using the Wilcoxon matched-pair signed-rank test. A + means that MSARC had a higher mean score while a − means MSARC had a lower mean score. Nonsignificant p-values (>0.05) are shown in parentheses.