Fig 1. A sequence of events in which individual i infects individuals j and then k (dashed arrows) along with the sampling of sequences taken from these individuals.

Solid circles represent the sequences at respective time points. Among these events only the sampling times $t_i^s$, $t_j^s$, $t_k^s$ and the corresponding sequence samples (coloured grey) are typically observed, while other unobserved quantities are to be imputed (see later). Other events potentially occurring on the dotted lines are not shown. Note that in our inference we do not demand that all exposures have an observed sequence. Also note that if individual i is a primary infection, G _1,i is assumed to be a stochastic variant of the universal master sequence G _M (see Multiple and Single Primary Infection Model).