Table 3.

Substitution rate matrix Q for the unrestricted model of nucleotide substitutions (UNREST).

	A	T	G	C
A	—	q AT	q AG	q AC
T	q TA	—	q TG	q TC
G	q GA	q GT	—	q GC
C	q CA	q CT	q CG	—

The diagonals of Q are determined to each row sum up to 0. The nucleotide stationary distribution π = (π _A, π _T, π _G, π _C) is given by the set of equations πQ = 0 under the constraint ∑_{i∈{A,T,G,C}} π _i = 1.