For running the provided software, you merely need the Java Runtime Environment (Version 1.5.0 or 5.0).
Microsoft Windows users just need to double-click the file called StandAlone.exe. Alternatively, you can double-click the file called StandAlone.bat, which requires the PATH variable to include the bin directory of the Java Runtime Environment.
Otherwise, execute the following command in the root directory created by the extraction of the zip file.
java -cp .;./lib/colt.jar;./lib/commons-collections-3.1.jar;./lib/commons-collections-testframework-3.1.jar;./lib/concurrent.jar;
./lib/jung-1.7.2.jar;./lib/junit.jar;./lib/postgresql-8.0-311.jdbc3.jar;./lib/resolver.jar;./lib/xercesImpl.jar;./lib/xml-apis.jar
-Xmx1024m gui.StandAlone
For testing the software, you can paste the contents of this FASTA file into the main text area, and specify 10 as the length and 40 as the score before clicking the button Next.