Table 1. BAliBASE results
AlignerAv score (218 families)BB11 (38 families)BB12 (44 families)BB2 (41 families)BB3 (30 families)BB4 (49 families)BB5 (16 families)Tot time (s)Consistency
MSAprobs0.6070.4410.8650.4640.6070.6220.60812 382.00Yes
Probalign0.5890.4530.8620.4390.5660.6030.54910 095.20Yes
MAFFT (auto)0.5880.4390.8310.4500.5810.6050.5911475.40Mostly (203/218)
Probcons0.5580.4170.8550.4060.5440.5320.57313 086.30Yes
Clustal Ω0.5540.3580.7890.4500.5750.5790.533539.91No
T‐Coffee0.5510.4100.8480.4020.4910.5450.58781 041.50Yes
Kalign0.5010.3650.7900.3600.4760.5040.43521.88No
MUSCLE0.4750.3180.8040.3500.4090.4500.460789.57No
MAFFT (default)0.4580.2580.7490.3160.4250.4800.49668.24No
FSA0.4190.2700.8180.1870.2590.4740.39853 648.10No
Dialign0.4150.2650.6960.2920.3120.4410.4253977.44No
PRANK0.3760.2230.6800.2570.3210.3600.356128 355.00No
ClustalW0.3740.2270.7120.2200.2720.3960.308766.47No
  • The figures are total column scores produced using bali score on core columns only. The average score over all families is given in the second column. The results for BAliBASE subgroupings are in columns 3–8. The total run time for all 218 families is given in the second last column. The last column indicates whether the method is consistency based.