Fig. 5

Estimation accuracy for gene rates in the OrthoMaM data set. Logarithmic scatterplots showing the 6,953 “reference” gene rates \(\hat {r}^{ML}_{k}\) estimated by Concat+ML (x-axis), against ratios \(\hat {r}_{k}/\hat {r}^{ML}_{k}\) (y-axis). Note that errors relative to the reference gene rates are measured with ratios, instead of differences. Colors (from blue to red) indicate increased density of points. The horizontal red line corresponds to no difference between the two estimates. Method names are shown at the top of each plot, followed by the mean absolute log-ratio between estimated and reference gene rates (see Additional file 3)