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

  • New (June 2011): Hypertree v1.2.2 adds basic support for phyloXML and better newick format integration and a few bug fixes.
  • Update (Oct 2008): Hypertree v1.2 provides improved printing, import of distance matrices and simple heat map drawing.
  • Update (Mar. 2008): Hypertree V1.1 includes numerous bug fixes and additional functionality.
  • Update (Mar 2008): Bug with license file now corrected.


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


HyperTree is freely available for non-commercial use. Download the Java jar file: HyperTree.zip, a sample tree file and a sample color file.

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

  1. On Macintosh or Windows, simply unzip the zip file and double-click the jar file to launch the program.
  2. On Unix and Linux, launch from the command line:
  3. java -jar HyperTree.jar


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.
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.


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 (PDF)