Additional file 1:

Included with this manuscript are the source code for SUP and documentation on both steps of the implementation described here. It is intended to be compiled on a UNIX/Linux system. On a Windows environment, the simplest way is to install CYGWIN http://www.cygwin.com webcite, a linux emulator. It compiles using gcc version 2.95.3 and higher. To install, type at the prompt % gunzip sup.tgz % tar -xvf sup.tar Go to the src/directory and compile by typing % make or % g++ *.cc -o sup The documentation can be found in the doc/directory. In there, scripts are included to help in the creation of input files. These scripts require perl and csh/tcsh.

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