Divide-and-Conquer Multiple Sequence Alignment Substitution Matrices

The following amino acid substitution matrices are currently supported by DCA. By clicking on the matrices in the table, the full matrices are shown:

substitution matrix	min. (lowest distance)	max. (highest distance)	gap function
PAM 250	0	25	$g(l) = 8 + 12\,l$
PAM 160	0	29	$g(l) = 8 + 12\,l$
Blosum 62	0	15	$g(l) = 6 + 10\,l$
Blosum 45	0	20	$g(l) = 10 + 9\,l$
Blosum 30	0	27	$g(l) = 10 + 11\,l$
Gonnet 250	0	19	$g(l) = 14 + 8\,l$
Gonnet 120	0	26	$g(l) = 17 + 10\,l$

Additionally, we provide a DNA/RNA substitution matrix accepting the complete IUPAC code and a unit cost distance matrix.

substitution matrix	min. (lowest distance)	max. (highest distance)	gap function
DNA/RNA	0	7	$g(l) = 15 + 3\,l$
unit cost	0	10	$g(l) = 0 + 10\,l$