Table 2.

Statistical probes used to match the simulated evolutionary history to a patient’s empirical HIV-1 env phylogeny.

Statistic	Type	Description
SI	Topological	The average number of splits from a tip to the root of a tree and captures asymmetry over the evolutionary history of the sample
MLT (Giardina et al. 2017; Janzen, Höhna, and Etienne 2015)	Time structure	The diversification of lineages normalized by the number of extant tips
EI ratio	Distance	The ratio between the mean external branch length (branch that ends with a sampling event) and the mean internal branch length (branch between coalescence events)
RPD	Distance	The difference in the empirical and simulated distributions of branch lengths ranked by size within each sampling event
CV in pairwise distance	Distance	The ratio between the standard deviation of pairwise distances between branches of the same sampling event and the mean pairwise distance between branches of the same sampling event

Notes: Some statistics measure tree characteristics (topological or time structure), while others measure distance statistics (distance). A simulation’s score, d, is the sum of the normalized differences between the statistic measured on reconstructed simulated tree and the empirical tree.