Viruses are designed to add their code to executable files of third party software, while worms simply add their files into system folders to be executed on system startup. Trojan horses – Allow computer to be controlled remotely; a hidden functionality user would not want.
Before we will dig deeper in those three phases - we have to make some important points: It is ongoing periodic work, not one time fix every change must be measured and its impact documented for the future it is not about Linux performance tuning (or FreeBSD, windows - any operating system), apache, mysql or other software components of the application - the main thing on which you will concentrate most efforts is your website. This is starting point and it is very important one – you always need to analyze your systems to know what is going on and why.
Client usually updates site's content using content management system and we take care of the rest: