Figure 3

Inferred and calculated acceptance rates of data sets simulated with SCPE. (a) local-score simulations. (b) global-score simulations. yn00 and yn00+w+f are two different methods to infer acceptance rates included in PAML (see Methods). The average acceptance rate inferred in the LPXA reference alignment (obtained with yn00+w+f) is 0.2246 ± 0.11. Using this value in (a) and (b) the optimal local and global λ obtained are 1.10 and 7.00, respectively. In (c) we plot the ω inferred using yn00+w+f versus the calculated value for SCPE runs from (a) and (b). The value inferred for the observed LPXA family is shown as a dotted line. Using this value the optimal ω for local score is 0.15(0.12–0.27) and for global score is 0.19(0.12–0.26).