SplitsTree4 is the leading application for computing evolutionary 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.

SplitsTree4 is an all-new implementation of the SplitsTree3 software written in Java. Superficially, this new program is similar to previous versions of this software. However, there are substantial differences. The new program has many new features, see the manual for details.

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.

Downloads

Use of the program requires a license. Licenses are freely available to all users. Obtain a license key online.
Download the latest version of the program here.

These installers do not contain a Java RunTime Environment (JRE). Please make sure that you have one installed, version 1.4.2 or higher.

Webstart

You can a run recent version of SplitsTree directly from within your web-browser by clicking here.

Manual

The most current version of the manual is available here.

Mailing list

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FAQs

Can I run SplitsTree with more memory?

Yes, under Linux invoke the program from a shell and provide the commandline option -J-Xmx1000M, say, to run the program with 1GB of memory.
Under Windows XP type the following DOS command: C:\\Programs\SplitsTree\SplitsTree.exe -J-Xmx1000M.
Under MacOS X, edit the file /Applications/SplitsTree/SplitsTree.app/Contents/Info.plist to add the option -Xmx1000M (say) to the key VMOptions.
Note that the limit is 1100M under Windows XP and 2000M under MacOS X or Linux.