Summary Tree Explorer

The Summary Tree Explorer (STE) is an open-source Java application for interactively exploring sets of phylogenetic trees using two coupled representations: a node-and-link diagram of a summary tree and a textual list of common clades, as shown in the figure below. Selection, pruning, filtering, or re-rooting in one representation is immediately reflected in the other. This Application Note provides more detail. STE accepts input files in NEXUS or Newick format, including files generated by MrBayes, PHYLIP, BAMBE, BADGER, and PAUP. Here is a more formal input file specification. STE does not accept weights on trees, so you must include the same tree multiple times to get that effect.

How to run the Summary Tree Explorer on your computer:

1. Make sure you have Java 1.4 or later installed. You can download the latest JRE here.
2. Download the following file to a local directory
   • http://cityscape.inf.cs.cmu.edu/phylogeny/phylogeny.jar
   • Optionally download example input files from http://cityscape.inf.cs.cmu.edu/phylogeny/Data/
3. Run the program:
   1. Open phylogeny.jar
   2. A "Load Forest" dialog box will open up, and you select the tree file you want to analyze. After that, you can switch to another file in the same directory using a menu.
   or
   1. From a command line or batch file, something like this

      java -Xmx256M -jar phylogeny.jar "C:\myTrees.nex" 100 1000

      • Change the "256" to give Java more or less than 256MB of memory.
      • If you provide your filename as an argument, it won't display the dialog box.
      • The last two optional arguments specify a "stride" and a "burn in." Only stride'th trees are read in, for example if stride is 3, it reads the zeroth, third, sixth, etc. The first burn-in'th trees are skipped. Burn-in 10 and stride 3 will read trees 12, 15, 18, etc. Using the gui, there are boxes to specify stride and burn-in to the right of the file choices. The default values are 1 and 0, which will read every tree.

Summary Tree Explorer is under active development; I will appreciate any comments you send to

or

Mark Derthick
Human Computer Interaction Institute
Carnegie Mellon University
Pittsburgh, PA 15213

Summary Tree Explorer has been supported by National Institutes of Health (NIH) grant R01 GM068950-01 and with the help of to Don Simon, Bret Larget, Jay Kadane, and David Baum. It is implemented in Piccolo, written by Ben Bederson at the University of Maryland HCIL.

Summary Tree Explorer version 12/2007, Copyright (C) 2007 Mark Derthick
Summary Tree Explorer comes with ABSOLUTELY NO WARRANTY; This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.