(**a**) The nodes, leaves and total accuracy of states reconstruction for simulations with varying transition rates and with fixed score distributions overlap value = 0.19. (**b**) The nodes, leaves and total accuracy of states reconstruction for fixed transition rate = 0.2 and varying score distributions overlap values. The red lines represent the tHMM results; the blue lines, BayesTraits results; the yellow lines, the results of dumbtHMM; and the green lines represent the results of the dumbtHMM reconstruction from the known assignment of states to leaves. The dashed lines show the accuracy for internal nodes reconstruction; the dotted line, the accuracy of leaves assignment (the yellow dotted line coincides with the blue dotted line); and the solid line, the mixed accuracy for all the nodes of the tree. (**c**) The number of reconstructed events normalized by the total tree length in the set for the same settings as in (**a**). (**d**) The number of reconstructed events normalized by the total tree length in the set for the settings as in (**b**). In (**c**) and (**d**), the green line represents the real number of events; the blue line, the number of events reconstructed by the BayesTraits algorithm; the red line, by the tHMM algorithm; and the yellow line, by the dumbtHMM algorithm. (**e**) The Matthews correlation coefficient(MCC) for the accuracy of events reconstruction for the same settings as in (**a**). (**f**) The MCC for the accuracy of events reconstruction number of reconstructed events for the settings as in (**b**). In (**e**) and (**f**), the green line represents the results of the dumbtHMM reconstruction from the known assignment of states to leaves; the blue line, the results of the BayesTraits algorithm; the red line, by the tHMM algorithm; and the yellow line, by the dumbtHMM algortihm.

## PubMed Commons