What Is A Rootkit?
At the core of the term "rootkit" are two words- "root" and "kit". Root refers to the all-powerful, "Administrator" account on Unix and Linux systems, and kit refers to a set of programs or utilities that allow someone to maintain root-level access to a computer. However, one other aspect of a rootkit, beyond maintaining root-level access, is that the presence of the rootkit should be undetectable.

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http://www.eeye.com/Resources/Security-Center/Research/Tools/BootRoot

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http://www.blackhatacademy.org/security101/index.php?title=Jynx