Estimation of TMRCA

Mean TMRCA values were estimated for each gene and each HCoV using PACT (Bedford et al., 2011). Briefly, PACT computes TMRCA values by creating a series of subtrees that include only tips positioned within a temporal slice of the full tree and finding the common ancestor of these tips. The overall mean and 95% confidence intervals were calculated from the list of TMRCA values in these time slices. The PACT config files and results for each run are in the directory antigenic_evolution/pact/. The TMRCA estimations and subsequent analyses are executed by code in antigenic_evolution/tmrca_pact.ipynb.