PhyD*: Fast NJ-like algorithms to deal with incomplete distance matrices.

Criscuolo A., Gascuel O.
BMC Bioinformatics. 2008, Mar 26;9:166.

Please cite THIS paper if you use PhyD*.

Files in the package


The program PhyD* is written in JAVA. To run JAVA, you should log on Java Technology Products Download, choose a Java Runtime Environment (e.g. JRE-5.0) and install those corresponding to your OS.

To use PhyD* with WINDOWS, you have to create a directory containing PhyDstar.jar, win_PhyDstar.bat and the input file. A simple double-click on win_PhyDstar.bat will launch the program.

With large distance matrix (e.g. > 5000 taxa), the java virtual machine does not allocate enough memory. To solve this problem, execute (with LINUX) the command line:
java -Xmx1024m -jar PhyDstar.jar
or edit and modify (with WINDOWS) the win_PhyDstar.bat file. This increases the memory space allocated to java up to 1024 Mb. Other values are possible (2048, 4096, ...).

© Copyright 2007 by Alexis Criscuolo and Olivier Gascuel.

The software is provided "as is" without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software, including but not limited to the frustration that you may experience in using the package. The program package, including source codes, example data sets, executables, and the user's guide, is distributed free of charge for academic use only.

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