Skip to main content

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