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Table 4 Comparison of average run time (in seconds) for the BAliBASE 3.0 benchmark dataset.

From: State of the art: refinement of multiple sequence alignments

BAliBASE reference alignments

ClustalW

Dialign

Mafft

 

Default

RASCAL

RF

REFINER

Default

RASCAL

RF

REFINER

Default

RASCAL

RF

REFINER

Reference 1

10.58

10.34

51.06

1.93

22.21

10.00

38.46

1.65

26.03

10.33

53.55

1.67

Reference 2

64.93

12.62

206.58

26.67

175.67

12.61

179.62

18.97

123.58

11.61

129.75

18.85

Reference 3

98.81

25.84

495.25

35.98

304.23

24.84

397.11

35.60

241.69

21.69

237.96

32.35

Reference 4

49.79

23.04

370.85

13.95

496.04

24.08

607.02

11.18

222.70

22.08

271.87

8.91

Reference 5

35.66

13.23

327.00

15.19

201.33

12.00

300.00

12.93

103.00

10.00

209.00

13.45

Average

51.95

17.01

290.15

18.74

239.90

16.71

304.44

16.07

143.40

15.14

180.43

15.05

BAliBASE reference alignments

Muscle

Probcons

T-Coffee

 

Default

RASCAL

RF

REFINER

Default

RASCAL

RF

REFINER

Default

RASCAL

RF

REFINER

Reference 1

23.21

10.00

49.83

2.09

29.34

10.54

38.67

2.37

20.54

10.62

36.79

1.73

Reference 2

116.66

12.20

124.50

16.10

167.12

12.25

170.50

13.47

160.74

21.23

166.29

18.34

Reference 3

267.28

24.84

261.86

36.76

289.49

20.84

283.72

31.38

284.11

21.78

265.29

38.84

Reference 4

267.70

24.58

272.55

11.00

362.29

22.08

443.12

11.26

403.40

12.08

415.00

7.57

Reference 5

111.00

8.00

215.00

20.41

203.00

8.00

206.00

15.64

188.00

10.00

232.00

14.03

Average

157.17

15.92

184.75

17.27

210.25

14.74

228.40

14.82

211.36

15.14

223.07

16.10