CXCR4 and infection: Since the sample population consisted of longitudinal samples from infections undergoing an HIV coreceptor switch, initially determined by a transition from NSI (non-syncytium inducing) to SI phenotypes, we also extracted the times to the MRCA of all observed sequences that were predicted to be CXCR4-using according to the g2p algorithm with a false positive rate (FPR) cutoff of 3.5.