Examples of RSA-dependent sequence-evolution models considered. All models have three parameters, evolutionary-rate ratio ω, branch length t, and transition–transversion ratio κ. All three parameters can be estimated as an individual value within each RSA bin (per-bin), as a linear function of RSA (linear), or as a constant across all RSA values (constant). The examples here are illustrated for n = 10 RSA bins. (A) All parameters are estimated per-bin. (B) ωis estimated as linear function, t is estimated per-bin, and κ is estimated as a constant. (C) All paramters are estimated as linear functions.