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The documentation is extracted directly from the sources, which makes it much easier to keep the documentation consistent with the source code.

There is also support for generating output in RTF (MS-Word), PostScript, hyperlinked PDF, compressed HTML, and Unix man pages. It can generate an on-line documentation browser (in HTML) and/or an off-line reference manual (in ) from a set of documented source files. Doxygen also supports the hardware description language VHDL. Doxygen is the de facto standard tool for generating documentation from annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba, Microsoft, and UNO/OpenOffice flavors), Fortran, and to some extent D.