HyperTree: hyperbolic phylogenetic tree viewer

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.

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

java -jar HyperTree.jar

Enjoy!

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

Mouse Controls

Reading and Writing Tree Files

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

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)