Illustration of all possible combinations of two binary characters (A and B) and the transition rates between these combinations.

The model fits rates for the transitions per infinitely small time interval and therefore allows the change of only one state at a time (i.e. no rates are fitted for diagonal transitions). The shaded character combinations are expected to dominate if characters A and B are positively correlated. This positive correlation is created by transition rates if ΔQ = q₂₁+q₂₃+q₄₁+q₄₃−(q₁₂+q₁₄+q₃₂+q₃₄)>0.