There are many simple methods for detecting an intrusion. Though they would only help you identify intruders who do not bother covering up their activities and traces.
In real scenario’s, you might need tools that are capable of doing much more. Many of these tools are to be installed in a clean OS and you need to constantly keep track of its reports, and act accordingly.
So, what if you do not have these intrusion detection tools installed already, and suspect something is wrong in your server. Some simple steps might help you here.