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A simple linear regression is used to estimate the rate of evolution assuming a strict molecular clock. To estimate the dates of the internal nodes, we follow an approach described by Felsenstein and motivated by TipDates Rambaut, A maximum likelihood method is applied locally to date each internal node. Then using these estimates, the algorithm iterates a specified number of times.
We compared these internal node dating results against a modified version of TempEst v1. However, the main purpose of TempEst is to detect or verify the presence of a strict molecular clock, not to date internal nodes Table 1.