Discrete Spatial Phylo-Simulator: Individual based modelling code for structured populations including phylogenetic tree outputs (in java).

The DiscreteSpatialPhyloSimulator is a java program which uses a stochastic individual based model to simulate infection over a structured population. The individuals are organised into "Demes", and Demes can be connected together in a variety of ways. Within a Deme all individuals have the same parameters, but each Deme could have its own particular parameters. For example, the DiscreteSpatialPhyloSimulator can be configured for:

* Phylogeography - each Deme is a location, individuals may migrate between locations.

* Zoonoses - each Deme is a species, infections may be transmitted between Demes, but the hosts themselves do not move.

* Networks - each Deme contains one host, infections may be transmitted between neighbouring Demes.