Embodiments of the present disclosure relate to anti-tamper computer systems, in particular to methods and systems which can embed protection code into software. Among other things, the protection code helps prevent (and make it more costly) to reverse engineer to tamper with the protected software with malicious intent, such as, but not restricted to: the removal of a license protection mechanism; the removal of code displaying advertisements; the injection of a malicious thread into the program memory space; illicit usage; or any other kind of unauthorized modification of the software.