SDM: a Fast Distance-based Approach for (Super)Tree Building in Phylogenomics.

Criscuolo A., Berry V., Douzery E.J.P., Gascuel O. Systematic Biology. 2006 55(5):740-755.

Please cite THIS paper if you use SDM.

Files in the package

Important

The program SDM 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.

SDM (and SDM*) proceeds by solving a system of linear equations. For this purpose, it uses the MTJ library (see the MTJ website for more informations). When downloading SDM, MTJ file (mtj.jar) is automatically downloaded in the same directory. Both mtj.jar and SDM.jar are zipped in file called SDM.tar, to be unzipped. To run SDM, mtj.jar and SDM.jar must always be in the same directory.

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

With large data collections (e.g., 50 distance matrices or trees defined by >100 taxa), the java virtual machine does not allocate enough memory. To solve this problem, execute (with LINUX) the command line: 
java -Xmx1024m -jar SDM.jar
or edit and modify (with WINDOWS) the win_SDM.bat file. This increases the memory space allocated to java up to 1024 Mb. Other values are possible (2048, 4096, ...).

© Copyright 2006 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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