Figure 1

General non-homogeneous model of substitution. The substitution model depicted here is Tamura's 1992 model of substitution, which contains two parameters: κ, the transitions/transversions ratio and θ the equilibrium G+C content. In the homogeneous case, θ and κ are constant over the tree (case 'a'). In Galtier and Gouy's 1998 model, κ is constant over the tree and one distinct θ is allowed per branch (case 'b'). Between these two extrema lay models with certain branches, but not all, sharing a common value of θ (case 'c'). In the most general case 'd', there are two sets of parameters, one for κ and another for θ, that are shared by the branches of the tree.