SplitsTree is a widely used application for computing unrooted phylogenetic networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks.
The current release is SplitsTree4.
(We wrote a new release, SplitsTree5, but that is an evolutionary dead-end.)
A complete overhaul of the SplitsTree4 program is now available as an "alpha" release (alpha means: expect many bugs, missing features and future changes): SplitsTree6. This new program will replace SplitsTree4 and Dendroscope3. It provides implementations of unrooted and rooted trees, unrooted and rooted networks, tanglegrams, consensus networks and densi-trees, and haplotype networks and phylogenetic outlines.
If you use SplitsTree in work in any way, then please cite the following paper: D. H. Huson and D. Bryant, Application of Phylogenetic Networks in Evolutionary Studies, Mol. Biol. Evol., 23(2):254-267, 2006.
Download the latest version of the program here.