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The X Windowing System, X11 (aka X, Xorg and, improperly, "Xwindows") is the low-level GUI subsystem on UNIX (except Mac OS), Linux and other operating systems.
X grew out of work on an earlier project called W, standing for "window". X provides support for windowing systems, and manages the mouse and keyboard during graphical sessions.
UNIX/Linux does not natively support GUIs, relying on a combination of X11 and toolkits such as Qt, GTK+ and Motif to do this. X provides tools to do these things but doesn't actually do them itself, all it takes care of is the actual rendering, getting stuff put on the screen. The toolkits interact with X11 to do things like draw scrollbars, buttons and the like.
This is in contrast to the method employed by MS Windows and Mac OSX where the toolkit, GUI subsystem and graphics primitives are part of the core operating system. Both methods have advantages and disadvantages. With X11 the toolkit do not currently take advantage of hardware acceleration if it is available (although individual programs can) and hardware acceleration in general has always been a Bear on X.
X11 is very old and creaky and urgent efforts to modernise and enhance it are under-way by the X.org foundation and FreeDesktop.Org project, subject to development politics.
An older implementation of X11--punningly called Xfree86--was done in by development politics giving rise to the X.org implementation that is now the standard on most major Unices including Linux and FreeBSD

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