 If we are given a starting (ancestral) state at one position, the model's "Q" matrix and a branch length expressing the expected number of changes to have occurred since the ancestor, then we can derive the probability of the descendant sequence having each of the four states.The mathematical details of this transformation from rate-matrix to probability matrix are described in the mathematics of substitution models section of the substitution model page.By expressing models in terms of the instantaneous rates of change we can avoid estimating a large numbers of parameters for each branch on a phylogenetic tree (or each comparison if the analysis involves many pairwise sequence comparisons).