Refined Buneman Trees

of Tübingen. In Dr. Husons words, SplitsTree is a program for analyzing and
visualizing evolutionary data.
The first version of SplitsTree was presented in an article from 1996 ([DHM96]),
and a later version followed in 1998 ([Hus98]). Up to version 3.2, SplitsTree was
written in C++, but starting from SplitsTree 4 the program will be developed in
Java. Versions have been incorporating more and more phylogenetic methods,
and this latest version features a plug-in facility which enables others to extend
the functionality of the program by adding new tree reconstruction methods and
analysis tools. The author has gratefully taken advantage of this in his work.
The JSplits program is available from this website:
http://www-ab.informatik.uni-tuebingen.de/software/jsplits/
In this work the author has used JSplits/ SplitsTree 4 version 3 beta,
but at the time of writing the JSplits development team has reach version 4 beta,
and the author is unsure whether this has introduced any inconsistencies.
11.2 Using JSplits
JSplits runs on any computer, Linux or Windows, with a JRE v1.4.2 (Java
Runtime Environment, available from http://www.java.com), which is very
handy indeed. It has a very simple user interface, as depicted in Figure 11.1.
To use JSplits to visualize a data set, one just opens the data set from a file, and
selects from a plethora of different tree methods using the drop down menus.
The result of applying a method to a dataset in JSplits is some graphical
representation depending on the method. For refined Buneman trees one gets
a tree graph with labeled leaves. It is possible to drag vertices to new positions
while keeping branch lengths constant, so one can sculpt the tree as one whishes.
It is also possible to zoom in on interesting regions, which is very useful for large
trees. The JSplits homepage might reveal more features, even some that the
author is not aware of, since JSplits development has raced ahead of this work.
One minor drawback to JSplits is that it only supports datasets in the Nexus
format. The test data used in this work, a set of protein families from the PFAM
database, is given in Phylip format, so it is not immediately applicable. However,
the translation from Phylip to Nexus is straghtforward, and the author
has written such a module (see chapter 12). The Nexus format is described in
[MSM97], but a simple google search will also provide several resources, including
format translation programs:
http://www.google.com/searchq=nexus+format
11.3 Extending JSplits
The implementation of the refined Buneman tree algorithm described in this
work is aimed at integration into JSplits. Java is perhaps not the first choice for
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