 GTR parameters consist of an equilibrium base frequency vector, formula_144, giving the frequency at which each base occurs at each site, and the rate matrix

Where

formula_146

are the transition rate parameters.Therefore, GTR (for four characters, as is often the case in phylogenetics) requires 6 substitution rate parameters, as well as 4 equilibrium base frequency parameters.However, this is usually eliminated down to 9 parameters plus formula_79, the overall number of substitutions per unit time.