Java TreeView can be run in one of three modes which can be selected at the time time that a file is opened. Each window within a running instance of java treeview has it's own mode.

Auto is selected by default, and tries to do a good job of picking the best mode for a file. This should be sufficient for most users.

Classic TreeView is similar to the visualization program by Michael Eisen([Eisen 1998]). It consists only of a dendrogram view of the data.

LinkedView is a generalization of TreeView. The idea is to present multiple linked visualizations of the same data which is present in TreeView. Initially, it shows a dendrogram view, but a Karyoscope View, ScatterView, as well as a new Alignment View can be show if the appropriate data is available.

KmeansView is a specialized version of TreeView for viewing the output of Michiel de la Hoon's Cluster 3.0 K-means clustering ([De Hoon 2002] , http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/) . This program is mostly similar to TreeView, although more k means-specific features could be added later.