The first methodology in doing penetration testing that is commonly used by people is the USSAF methodology. The ISSAF is the flagship project of the OISSG with the latest version is the version 0.2 that is available for any industry need to do this testing. This methodology is the first one that provides such validation for the bottom up strategies of the security. The next famous methodology of this testing is the OSSTMM which is Open Source Security Testing Methodology Manual. This one is a peer-reviewed security metrics and tests methodology.
There are five channels available on this methodology in conducting the security test to maximize the result including the data & information controls and also security awareness level of the personnel as well. The last one is the Open Web Application Security Project or the OWASP. This is an open-source security application project of the OWASP community. This community provides methodologies, tools, technologies, documentations, and also articles related to the testing of security on a particular system. All of those three are the most commonly used methodologies in conducting the testing of the network or computer security system known as the penetration testing.
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