NETGEN: generating phylogenetic networks with diploid hybrids.

SUMMARY: NetGen is an event-driven simulator that creates phylogenetic networks by extending the birth-death model to include diploid hybridizations. DNA sequences are evolved in conjunction with the topology, enabling hybridization decisions to be based on contemporary evolutionary distances. NetGen supports variable rate lineages, root sequence specification, outgroup generation and many other options. This note describes the NetGen application and proposes an extension of the Newick format to accommodate phylogenetic networks. AVAILABILITY: NetGen is written in C and is available in source form at http://www.phylo.unm.edu/~morin/.