Here is how to install 2 popular tools for scanning your servers for rootkits, trojans:
RKHunter
http://rkhunter.sourceforge.net/
Install
wget http://downloads.sourceforge.net/project/rkhunter/rkhunter/1.3.8/rkhunter-1.3.8.tar.gz
tar -xvzf rkhunter-1.3.8.tar.gz
cd rkhunter-1.3.8
./installer.sh –install
rkhunter –propupd
Scan
rkhunter –check
Also check resulting log in /var/log/rkhunter.log .
ChkRootkit
http://www.chkrootkit.org/
Install
wget ftp://ftp.pangeia.com.br/pub/seg/pac/chkrootkit.tar.gz
tar xvzf chkrootkit.tar.gz
cd chkrootkit*
make sense
Scan
./chkrootkit
