First, install fierwall (APF or configserver security and firewall) and then install Root kit checker (chkrootkit).
To install chkrootkit, SSH into server and login as root.
At command prompt type:
cd /root/ (any location where you would like to install it)
wget
ftp://ftp.pangeia.com.br/pub/seg/pac/chkrootkit.tar.gztar xvzf chkrootkit.tar.gz
cd chkrootkit-0.44
make sense
To run chkrootkit
At command prompt type:
/root/chkrootkit-0.44/chkrootkit
Also set the cron to run chrootkit on regular basis and keep the version of chkrootkit updated.