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Table 1 Impact on alignment quality following refinement.

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 0.65 0.63 0.66 0.66 0.62 0.65 0.67 0.62 0.70 0.69 0.69 0.71
Reference 2 0.78 0.80 0.80 0.80 0.78 0.80 0.79 0.79 0.83 0.82 0.83 0.82
Reference 3 0.66 0.69 0.67 0.68 0.65 0.64 0.65 0.66 0.76 0.73 0.75 0.77
Reference 4 0.67 0.68 0.66 0.70 0.67 0.71 0.66 0.69 0.75 0.73 0.70 0.77
Reference 5 0.65 0.67 0.66 0.68 0.67 0.65 0.64 0.67 0.76 0.73 0.72 0.76
Average 0.682 0.694 0.69 0.704 0.678 0.690 0.682 0.692 0.760 0.740 0.738 0.766
Increment (%) 0 1.760 1.173 3.226 0.000 1.770 0.590 2.065 0.000 -2.632 -2.895 0.789
BAliBASE reference alignments Muscle Probcons T-Coffee
  Default RASCAL RF REFINER Default RASCAL RF REFINER Default RASCAL RF REFINER
Reference 1 0.66 0.66 0.67 0.67 0.72 0.72 0.70 0.73 0.68 0.68 0.69 0.68
Reference 2 0.80 0.81 0.80 0.80 0.83 0.83 0.82 0.82 0.81 0.83 0.82 0.82
Reference 3 0.71 0.71 0.71 0.73 0.76 0.73 0.75 0.77 0.63 0.62 0.62 0.64
Reference 4 0.71 0.72 0.68 0.72 0.77 0.75 0.71 0.77 0.71 0.71 0.70 0.72
Reference 5 0.70 0.71 0.67 0.71 0.76 0.74 0.71 0.75 0.73 0.73 0.69 0.74
Average 0.716 0.722 0.706 0.734 0.768 0.754 0.738 0.77 0.704 0.714 0.704 0.720
Increment (%) 0.000 0.838 -1.397 2.514 0.000 -1.823 -3.906 0.260 0.000 1.420 0.000 2.273