Table 4

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

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


Chakrabarti et al. BMC Bioinformatics 2006 7:499   doi:10.1186/1471-2105-7-499

Open Data