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Pairwise estimates of ω = dN/dS, d, dS, and dN for sequence alignments simulated using a model of constant ω among sites (A–C) or using a mixture model of variable ω among sites (A′–C′), using parameter estimates from the 244-species mammalian mitochondrial gene alignment. (A and A′) Pairwise estimates of ω vs. d. (B and B′) Pairwise estimates of dS vs. d. (C and C′) Pairwise estimates of dN vs. d.
