Simulating trajectories | Building the simulator | Defining simulations parameters | Running simulations | Direct method | $\tau$-leap method | Mixed method | Trajectory in output file | Simulating phylogenies | Multiple demes | Initialising the system | Tau-leap trajectory simulation | Phylogeny simulation | With known sampling dates and known proportion of sampling | With known sampling dates, each assigned to a compartment by the user | With only known sampling dates | References