downloads
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bwa-1.0.jar
A precompiled jar file, ready to be added to your $CLASSPATH. (However, you still need to install Soot 2.2.1) For details see the INSTALL file.
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bwa-1.0.src.tar.gz
The sources for compilation with javac (Ant build.xml included; also generates API documentation and the above jar file). Extract them and follow the instructions contained in the INSTALL file.