How to set ASP.NET version to 3.5 in the IIS 6 Default Web site properties (ASP.NET tab)? From what I can see was version 2 (even though I have install version .NET 3.5)

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You cannot specify this in IIS. For websites earlier than Framework 4.0 and greater than 2.0 you need to specify version 2.0 in IIS.
However there are configurations in web.config to restrict a website to run or compile under framework version 3.5. Visual Studio by default make these setting in web.config
To be sure here are some parts of the web.config