Bayesian phylogenetic analyses of WGS facts from EPICC cohort had been done applying BEAST21. The product we utilized was comparable to the CRC phylogenetic analyses reported before2. We generated an input XML file for BEAST2 with BEAUti. The product and parameters we utilized are as beneath: as all clones were sampled concurrently, we set all idea dates as 0; as for that substitution design, we used the GTR model and set the Gamma Class Count to 4; we utilised the “Comfortable Clock Exponential” as clock model; As for prior for the peaceful clock charge indicate, we applied four.
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