HyperTree

HYPERTREE is a Java phylogenetic tree viewer, with a hyperbolic ('fish-eye') view and editing abilities that help in managing very large trees.

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.jar.gz
       HyperTree source (.zip file)
       HyperTree V1
       A sample tree and color file

To run the program, you must have Java 2 or higher installed.

1. On Macintosh or Windows, simply double-click the jar file to launch the program.
2. 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
• The demo version of HyperTree displays a tree of C. elegans protein kinases. It cannot save modifications to this tree or open any other tree files
• HyperTree reads and saves trees in Phylip format
• It 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, such as the data retrieval tool.

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.

Citation

Visualizing harge hierarchical clusters in hyperbolic space
J. Bingham, S Sudarsanam
Bioinformatics (2000) 16(7): 660-1 (PDF)