Table 2.

The matrix test sets assessed in the homology search performance evaluation

Test set	Algorithm	Matrix numbers
PFASUM Search Matrices	PFASUM	[11,100]
Standard Search Matrices	BLOSUM	50,62,80
	MD	10,20,40
	Optima	5
	PAM	120,250
	VTML	10,20,40,80,120,160,200