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
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
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
- 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 color2Node 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
- To rotate the tree, drag while holding down the shift key.
HyperTree was written by Jonathan Bingham of Sugen, Inc. and is made freely available for non-commercial use.
CitationIf 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)