According to Wikipedia, A root kit is a set of tools used by an intruder after cracking a computer system. These tools can help the attacker maintain his or her access to the system and use it for malicious purposes.
It is pretty hard to detect a root kit using standard system tools so we need to use specialized detection programs. Below are links to software that detects RootKits in Linux:
Rootkit Hunter scans files and systems for known and unknown rootkits, backdoors, and sniffers. The package contains one shell script, a few text-based databases, and optional Perl modules. It should run on almost every Unix clone.
chkrootkit is a tool to locally check for signs of a Rootkit.