Table 2.

Comparison of multiple sequence alignment methods

	SP/TC scores								Computation
Aligner	All	XX-XX RV11	XX-XX RV12	XX-XX RV20	XX-XX RV30	XX-XX RV40	XX-XX RV50	XX-XX BB40037	Time
Non-progressive methods
MSARC	$$\frac{87.6}{57.1}$$	$$\frac{\mathbf{69}.9}{\mathbf{46}.3}$$	$$\frac{94.5}{85.7}$$	$$\frac{92.5}{39.2}$$	$$\frac{83.7}{47.2}$$	$$\frac{\mathbf{93}.2}{62.3}$$	$$\frac{88.7}{51.6}$$	$$\frac{\mathbf{98}.7}{\mathbf{70}.0}$$	16:36:37
DIALIGN-T	$$\frac{77.3}{42.8}$$	$$\frac{49.3}{25.3}$$	$$\frac{88.8}{72.5}$$	$$\frac{86.3}{29.2}$$	$$\frac{74.7}{34.9}$$	$$\frac{82.0}{45.2}$$	$$\frac{80.1}{44.2}$$	$$\frac{52.6}{0.0}$$	1:13:21
FSA	$$\frac{78.5}{42.1}$$	$$\frac{50.3}{26.9}$$	$$\frac{92.4}{81.8}$$	$$\frac{86.7}{18.7}$$	$$\frac{70.7}{27.6}$$	$$\frac{85.5}{46.2}$$	$$\frac{78.2}{39.8}$$	$$\frac{81.8}{30.0}$$	35:15:34
PicXAA	$$\frac{\mathbf{87}.8}{59.4}$$	$$\frac{69.0}{\mathbf{46}.3}$$	$$\frac{94.6}{86.2}$$	$$\frac{92.5}{41.6}$$	$$\frac{86.0}{59.8}$$	$$\frac{93.1}{\mathbf{62}.4}$$	$$\frac{89.2}{53.0}$$	$$\frac{\mathbf{98}.7}{\mathbf{70}.0}$$	5:54:18
Progressive methods
CLUSTAL Ω	$$\frac{84.0}{55.4}$$	$$\frac{59.0}{35.8}$$	$$\frac{90.6}{78.9}$$	$$\frac{90.2}{45.0}$$	$$\frac{86.2}{57.5}$$	$$\frac{90.2}{57.9}$$	$$\frac{86.2}{53.3}$$	$$\frac{61.2}{0.0}$$	12:15
DIALIGN-TX	$$\frac{78.8}{44.3}$$	$$\frac{51.5}{26.5}$$	$$\frac{89.2}{75.2}$$	$$\frac{87.9}{30.5}$$	$$\frac{76.2}{38.5}$$	$$\frac{83.6}{44.8}$$	$$\frac{82.3}{46.6}$$	$$\frac{52.8}{0.0}$$	1:36:05
MAFFT	$$\frac{86.7}{58.4}$$	$$\frac{65.3}{42.8}$$	$$\frac{93.6}{83.8}$$	$$\frac{92.5}{44.6}$$	$$\frac{85.9}{58.1}$$	$$\frac{91.5}{59.0}$$	$$\frac{90.1}{59.4}$$	$$\frac{56.4}{0.0}$$	54:04
MSAProbs	$$\frac{\mathbf{87}.8}{\mathbf{60}.7}$$	$$\frac{68.2}{44.1}$$	$$\frac{\mathbf{94}.6}{\mathbf{86}.5}$$	$$\frac{\mathbf{92}.8}{\mathbf{46}.4}$$	$$\frac{\mathbf{86}.5}{\mathbf{60}.7}$$	$$\frac{92.5}{62.2}$$	$$\frac{\mathbf{90}.8}{\mathbf{60}.8}$$	$$\frac{59.5}{0.0}$$	6:43:51
MUSCLE	$$\frac{81.9}{47.5}$$	$$\frac{57.2}{31.8}$$	$$\frac{91.5}{80.4}$$	$$\frac{88.9}{35.0}$$	$$\frac{81.4}{40.9}$$	$$\frac{86.5}{45.0}$$	$$\frac{83.5}{45.9}$$	$$\frac{48.4}{0.0}$$	23:32
Probalign	$$\frac{87.6}{58.9}$$	$$\frac{69.5}{45.3}$$	$$\frac{\mathbf{94}.6}{86.2}$$	$$\frac{92.6}{43.9}$$	$$\frac{85.3}{56.6}$$	$$\frac{92.2}{60.3}$$	$$\frac{88.7}{54.9}$$	$$\frac{54.2}{0.0}$$	4:31:41
ProbCons	$$\frac{86.4}{55.8}$$	$$\frac{67.0}{41.7}$$	$$\frac{94.1}{85.5}$$	$$\frac{91.7}{40.6}$$	$$\frac{84.5}{54.4}$$	$$\frac{90.3}{53.2}$$	$$\frac{89.4}{57.3}$$	$$\frac{59.3}{0.0}$$	6:56:32
T-Coffee	$$\frac{85.7}{55.1}$$	$$\frac{65.5}{40.9}$$	$$\frac{93.9}{84.8}$$	$$\frac{91.4}{40.1}$$	$$\frac{83.7}{49.0}$$	$$\frac{89.2}{54.5}$$	$$\frac{89.4}{58.5}$$	$$\frac{50.9}{0.0}$$	13:53:02

Columns 2-9 show the mean SP and TC scores for each alignment algorithm on the whole BAliBASE 3.0 dataset, each of its series and case BB40037. The last column presents total CPU computation time (hh:mm:ss). All scores are multiplied by 100. Best results in each column are shown in bold.