Centroid Wheel Tree

Centroid Wheel Tree is an Intuitive, Informative, and Most Balanced representation of phylogenetic trees.

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Contact

Wataru IWASAKI
Dept. Biological Sciences,
Grad. Sch. Science,
University of Tokyo, Japan
E-mail:
iwasaki AT bs.s.u-tokyo.ac.jp

Licenses

CWT Software:
GNU General Public License
The other content:
Creative Commons License

Download Software

To run the program locally,

1. Install Java SE 5.0 or higher if not installed (Command java -version will tell you its availability). Java is available at the Java website

2. Download and put the following files to the same directory:
i) CentroidWheelTree.jar
ii) concorde or concorde.exe (Executable files): available at the Concorde website
iii) phyutility.jar: The source code and the latest version may be available at the Phyutility website (The jar file we distribute is version 2.2)
iv) xmlgraphics-commons-1.3.1.jar and
v) commons-io-1.3.1.jar: The latest versions may be available at the Apache XML Graphics Commons website
vi) args4j-2.0.12.jar: The latest version may be available at the Args4j website

3. Then, the command
java -jar CentroidWheelTree.jar [-a N] [-c] [-d] [-r] [-s] [-t] PathToTreeFile
-a N : Threshold support in building consensus tree (Default 75. Input >100 for star-like tree)
-c : Use color visualization (ignored if -d is used)
-d : Show average distances
-r : Use rooted trees
-s : Show strict supports
-t : Output only topologies
will produce .nhx, .ps, and .png files, with some intermediate files and log files.
Refer to Examples and NHX Format for interpretation of the CWT files.

Notes:
For sample input tree files, visit the Execute on Web page.
If newer versions of the jar archives are used, classpaths must be set explicitly.

This software is available under the GNU General Public License, and its source code is available here.