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 are currently working on SplitsTreed5 and a preview version is available here: Download SplitsTree5
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.