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I have looked at this question already but a graphical representation is not exactly what I want.

Is there a SOOT like tool for Javascript that gives you an intermediate representation you can play with? Or else, is there a Javascript -> Java-bytecode -> Javascript converter? (so that I can use SOOT with Java-bytecode to do my transformations and get it back as Javascript)

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I don't think such a tool exists. WALA can analyze JS to some extent but it cannot generate JS code again. Many people I know who analyze JS do this by modifying a JIT compiler.

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Closure Compiler by Google comes close. They are using Rhino's intermediate representation and treating code rewrite as string composition.

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