Initialization | What's in a state | Running the simulation | Tricks for complex setups | Cleaning up the simulation

Sample data | Trees | Sequences (fasta) | Pairwise distance matrices | Tree-based distance matrix | Sequence-based distance matrix

Simulator outputs. | Internal representations of trees

Simulation | The simulation API | Removing individuals from the active population | A simple example | Reporting the entire history of the simulation

Independent random sampling | Proportional sampling | Exhaust a single cluster | High contact tracing | Low contact tracing | Multiple clusters

Simulate a transmission network with gen_transmission_history_exponential_constant | Exponential growth / offspring generation rate | Maximum target population size | Minimum population | Length of the constant growth phase | Sample a collection of tips | Extract the subtree | Exporting | Newick string or ape tree | Pairwise distance matrix