OSSEC HIDS will perform rootkit detection on every system where the agent is installed. The rootcheck (rootkit detection engine) will be executed every X minutes (user specified - by default every 2 hours) to detect any possible rootkit installed. Used with the log analysis and the integrity checking engine, it will become a very powerful monitoring solution.
These configuration options can be specified in each agent’s ossec.conf, except auto_ignore and alert_new_file which are manager side options. If the ignore option is specified on the manager the setting becomes global for all agents.