As part of my dissertation, I developed three separate pieces of software related to phylogenetic networks. Generally speaking, a phylogeny is an evolutionary history (either simulated, hypothesized, or even tracked on a small scale). Representations of such often have a "tree" structure. However, it is possible for interactions to occur -- causing a "network" to be formed. My work involved supporting the inclusion (and assessing the impact) of hybrids to common phylogenetic tasks such as simulation and reconstruction. The most recent versions of the three software pieces are provided below.
Two citations for this work are:
Morin, M. M. "Phylogenetic Networks: Simulation, Characterization, and Reconstruction," Disssertation, University of New Mexico, Department of Computer Science (2007). (ps gzipped ps pdf)
Morin, M.M. and Moret, B.M.E. "NetGen: generating phylogenetic networks with diploid hybrids," Bioinformatics 22 (2006), 1921-1923. pdf preprint
NetGen and NSGW facilitate simulating phylogenetic networks.
NetMeasure calculates three node-level characteristics and the extended RF distance.
NetReconstruct proposes and constructs phylogenetic networks containing a single diploid hybrid.
For simply the release notes (each as a separate PDF):NetGen NSGW NetMeasure NetReconstruct
To download software and notes for each component (each as a gzipped tar file -- most recent version is Kappa):NetGen NetMeasure NetReconstruct
Important notes about supporting software:
NetGen requires Seq-Gen to simulate DNA sequences. Here is a copy of Seq-Gen version 1.3.2 (compressed file): Seq-Gen. More information can be found about Seq-Gen from the Molecular evolution, phylogenetics, and epidemiology site. (It is assumed Seq-Gen will be installed as part of the NETGEN subdirectory structure. This is necessary as communication between the simulator and Seq-Gen occurs multiple times via pipes. Details can be found in the release notes.)
NetReconstruct requires PHYLIP to reconstruct subtrees. PHYLIP software and information can be found