FEATURES

HyperTree includes many features for navigating large trees, such as the ability to:

• visualize large trees with hundreds of nodes or more
• rotate and drag the display in cartesian space
• search and select nodes
• copy clusters for pasting into other programs
• color-code branches
• label branches (eg, common family members)
• zoom in and out
• view phylogenetic trees and other hierarchical clusters, such as gene expression profile clusters
• run on several platforms: Mac, Windows, Unix/Linux

DOWNLOAD

HyperTree is freely available for non-commercial use. The download includes the Java jar file, source code and sample files.

To run the program, you must have Java 5 or higher installed.

On Macintosh or Windows, simply double-click the jar file to launch the program. On Unix and Linux, launch from the command line: java -jar HyperTree.jar Enjoy!

USAGE TIPS

Currently no comprehensive usage manual exists for HyperTree. However, here is a brief summary of 'non-obvious' features.

Mouse Controls

• To rotate the tree, drag while holding down the shift key.

Reading and Writing Tree Files

• HyperTree reads trees in Phylip, Newick and phyloXML formats.
• HyperTree can also generate a tree from a distance matrix. Use: File -> Import Distance Matrix
• HyperTree saves trees in Phylip/Newick format.
• HyperTree displays one tree at a time; if a file contains multiple trees, only the first tree will be displayed.

Selecting Nodes and Branches

• Labels appear on mouseover
• Click a label or node to select it
• Hold down the "SHIFT" or "CTRL" key when clicking to add multiple selections
• Select an internal node and then choose "Select Children" to select an entire subtree
• Click "Copy" or "CTRL C" to copy all selections to the system clipboard. Then you can paste them into other programs as Phylip/Newick trees.

Colorizing the Tree

• Choose "Color" to change the color of all selected labels and nodes
• Choose "Export Colors" from the "File" menu to save the colors

You can create a color file independently of HyperTree. To import a color file, choose "Import Colors" from the "File" menu. A valid color file has the following format: nodeLabel1 color1 nodeLabel2 color2

Node labels are case-sensitive. They must exactly match the labels in the tree. Node labels are separated by white space from the color.

Colors can be specified in the color file in one of three ways. A color can be either an RGB value, a color name in plain English using any of the standard color names recognized by Netscape and Internet Explorer; or an arbitrary identifier, in which case HyperTree will attempt to automatically assign a color by default. E.g., ZC123.4 darkGreen ZC239.7 0,0,255 ZC373.4 tyrosineKinase

HyperTree was written by Jonathan Bingham of Sugen, Inc. and is made freely available for non-commercial use.

CITATIONS

If you use Hypertree in a publication, please cite: Visualizing harge hierarchical clusters in hyperbolic space J. Bingham, S Sudarsanam Bioinformatics (2000) 16(7): 660-1