Table 1 Notation used in this article
Embedded ImageTransmission route from person i to person j
Embedded ImageTime of infection of person j
Embedded ImageTime of genome sampling from person j
Embedded ImageVector of transmission ancestry common to persons i and j
Embedded ImageTime of lineage divergence
μMutation rate per genome per generation
Embedded ImageGenetic distance (no. SNPs) between genomes a and b
Embedded ImageCoalescence time of isolates a and b
Embedded ImageTime between coalescence and observation time t
Embedded ImageEffective pathogen population size at time t
Embedded ImageEffective transmission bottleneck size