General Workflow

1. The contact network is generated (nodes: individuals; edges: contacts).
2. Seed individuals who are infected at time 0 are selected (2a), and a viral sequence is chosen for each (2b).
3. The epidemic yields a series of transmission events in which the time of the next transmission is chosen (3a), the source and target individuals are chosen (3b), the viral phylogeny in the source node is evolved to the transmission time (3c), viral sequences in the source node are evolved to the transmission time (3d), and a viral lineage is chosen to be transmitted from source to destination (3e). Step (3) repeats until the end criterion is met. Step 3c–3e are optional, as tree and sequence generation can be delayed to later steps.
4. Infected individuals are sampled such that viral sequencing times are chosen for each infected individual (4a), viral phylogenies (one per seed) are evolved to the end time of the simulation (4b), and viral phylogenies (one per seed) are pruned to reflect the viral sequencing times selected (4c).
5. Mutation rates are introduced along the branches of the viral phylogenies and the tree is scaled to the unit of expected mutations.
6. The seed trees are merged using a seed tree (cyan).
7. Viral sequences obtained from each infected individual are finalized.
8. Real-world errors are introduced on the error-free data, such as subsampling of the sequenced individuals (marked as green) (8a) and the introduction of sequencing errors (8b).