Disclaimer: These applications have been successfully tested on Windows XP Professional and Mac OS X using Firefox, Opera, IE, and Netscape, and Safari. We cannot guarantee that untested platforms or browsers will correctly display the applications below.
At this time we are not actively developing tree-visualization routines for mor. In the future, we hope to implement some of the excellent tools that are being devloped elsewhere, such as Dendroscope (http://www-ab.informatik.uni-tuebingen.de/software/welcome.html), PhyloWidget (http://www.phylowidget.org) among several other programs out there. In the meantime, you will have to continue to use our simple trees which are generated from the output of PAUP* or download the tree files for your own use.
Visualization of large phylogenetic trees, such as those created by mor, is challenging, because these trees contain large quantities of information that reside at multiple hierarchical levels (i.e., relationships among terminal taxa, as well as higher-level relationships among major clades). Currently, mor addresses this challenge by creating clade viewer pages, which present the topologies of individual clades, along with information specific to those clades. However, it is already difficult to view some clades in their entirety, such as the euagarics clade (presently 1265 sequences) and the bolete clade (328 sequences). In addition, while it is possible to surf from the clade viewer pages to other clades in the global tree (using links appended to terminal sequences), this is not as convenient as we would like. Ideally, one would like a mechanism that allows one to scan the higher-order topology created by mor (which contained 2401 sequences, as of April 9th, 2005) and zoom in selectively to view specific groups in detail.
Several applications have recently been developed to meet the challenges of tree visualization, including accordion trees and hyperbolic trees. Both of these approaches allow large trees to be compressed and expanded graphically, such that the entire topology can be viewed on a single screen. We are experimenting with several applications to visualize the trees produced by mor. While the trees that we have produced lack much of the functionality of the trees in the clade viewer pages, they demonstrate the potential for these approaches to facilitate interaction with large trees. Below, the mor tree of April 9th, 2005 is presented by the programs TreeJuxtaposer, ATV, and Treebolic.
Tree Juxtaposer (References)
TreeJuxtaposer is an application written in Java/OpenGL that was designed by Tamara Munzner and her lab members. TJ produces accordion trees, using a mechanism that mimics fish-eye distortion. Since TJ currently cannot be run as an applet, we have created a package that can be downloaded. It contains TreeJuxtaposer, mor's dataset, and instructions on how to use it. For current information about TJ, please visit the Munzner lab web site.
ATV is an application developed in Sean Eddy's laboratory by Christian Zmasek. ATV is written in Java and can be used as an applet, a program that runs through a web page. Since it can be run as an applet, ATV is simpler to use than many other tree visualization programs. Features include the ability to zoom, collapse subtrees, and display desired elements of the tree. For more information about ATV, please visit ATV- a phylogenetic tree display tool.
Treebolic is a program developed by Bernard Bou that can generate a hyperbolic tree and display the result as an applet. Treebolic is available on sourceforge at the Treebolic home. Hyperbolic trees employ distortion methods that some viewers may not find very intuitive. We find that it is easy to lose track of the relative locations of nodes in the tree. Nevertheless, hyperbolic trees are highly interactive and with practice they provide an efficient means to examine the structure of large phylogenetic trees.
TJ ReferencesTreeJuxtaposer: Scalable Tree Comparison using Focus+Context with Guaranteed Visibility
TreeJuxtaposer: Scalable Tree Comparison using Focus+Context with Guaranteed Visibility (pdf)
TreeJuxtaposer: InfoVis03 Contest Entry
Scalable, Robust Visualization of Large Trees (expansion of TJ capabilities)
Tamara Munzner lab homepage
ATV: Display and Manipulation of Annotated Phylogenetic Trees (pdf)
ATV - a phylogenetic tree display tool