SplitsTree

SplitsTree is an exceptional tool for computing unrooted phylogenetic networks from molecular sequence data. With its ability to work with alignments of sequences, a set of trees, or a distance matrix, it efficiently computes phylogenetic trees or networks using an array of methods. These methods include split decomposition, consensus network, neighbor-net, super networks, as well as hybrid computing methods.

The software is written in the widely used programming language, Java. One of the main advantages of using Java is that it is cross-platform, and thus the program can run on various operating systems, such as Linux, MacOS, Windows, and Unix. This feature also allows for the integration of plug-ins that add new functionality to the program, like import or export modules, as well as new methods.

However, using Java to implement algorithms can make them run slower compared to C or C++. Therefore, while the program has many benefits, the speed of certain tasks should be taken into account before use.

It is also essential to note that you must have a license to use SplitsTree4, which you can get from the link provided on the official website. In conclusion, SplitsTree offers many advanced features for computing phylogenetic networks that make it an exceptional tool for researchers in the field.