Software for computing phylogenetic networks
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 have written a new, open source program call SplitsTree Community Edition, SplitsTreeCE. This is currently under rapid development. We are currently calling this a "beta" release, which means that we are making this available for testing and feedback. We plan to wrapup programming and to submit a publication by the end of March 2023. 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 your work, 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.