Table 2.

The alignment programs which obtained the highest AQ, SP and CS scores in different reference sets.

	Top Programs
Reference set	AQ	SP	CS
11	Probcons, L-INS-i, Muscle	ProbCons	ProbCons, L-INS-i
12	Probcons, Muscle, L-INS-i, Tcoffee	ProbCons	ProbCons
20	L-INS-i, Clustal, Muscle, Tcoffee	ProbCons	ProbCons, L-INS-i
30	L-INS-i, Clustal, TCoffee, FFT-NS-2, Muscle, Probcons	L-INS-i, Probcons, Muscle, TCoffee	L-INS-i, Probcons, TCoffee, Muscle
40	L-INS-i, TCoffee	L-INS-i, Probcons, TCoffee	L-INS-i, TCoffee, Probcons
50	L-INS-i, TCoffee, Probcons, Muscle, FFT-NS-2, Clustal	TCoffee, Probcons, L-INS-i	L-INS-i, TCoffee, Probcons, Muscle

The programs have no statistically significant differences between each other in the particular set. Statistical analyses were performed using Wilcoxon signed rank test.