Data from: The local-clock permutation test: a simple test to compare rates of molecular evolution on phylogenetic trees

Rates of molecular evolution vary substantially between lineages, and a growing research effort is directed at uncovering the causes and consequences of this variation. Comparing local-clocks (rates of molecular evolution estimated from sets of branches of a phylogenetic tree) is a common tool in this research effort. Here, I show that a commonly used test (the Likelihood Ratio Test, LRT) will not be statistically valid for comparing local-clocks in most cases. Instead, I propose the local-clock permutation test (LCPT), a simple test which can be used to test the significance of differences between local-clocks. The LCPT could also be used to test for differences between any parameter that can be assigned to individual branches on a phylogenetic tree. Using simulated data, I show that the LCPT has good power to detect differences between local-clocks.LCPT_simulation_filesThis zipfile will unzip to produce a folder which contains all the files and python script necessary to run all the simulations in the paper. Detailed instructions on how to replicate the analyses in the paper are provided in the README, and at the top of the python script in the file (open it in a text editor)