Table 1. Average performance in terms of the AUC and AUC01 values of the three methods: Max-Freq, Shannon, and Kullback-Leibler described to measure conservation.

Conservation measure	Max-Freq		Shannon		Kullback-Leibler
	AUC	AUC01	AUC	AUC01	AUC	AUC01
Raw	0.874	0.458	0.880	0.464	0.892	0.485
C	0.870	0.461	0.876	0.465	0.890	0.502
L	0.857	0.380	0.852	0.371	0.877	0.437
Cl	0.847	0.353	0.837	0.335	0.868	0.411

Each measurement is applied under four conditions defined by sequence weighting using clustering (c); pseudo count correction using low counts (l), the combination of the two (cl), and no correction (raw). In bold is highlighted the method with the highest performance for each performance measure.