Lynis is an open-source security auditing tool for UNIX-based systems. It performs an in-depth security scan and is primarily used to test security defenses and provide insight for further system hardening as well as scanning for general system information, vulnerable software packages, and possible configuration issues. It also scans for security information, installed and available software information, configuration mistakes, security issues, user accounts without a password, wrong file permissions, firewall auditing.
Rootkits give people the ability to remotely control your computer. Sometimes they can be difficult to detect and are even harder to remove. Chkrootkit is a tool to locally check for signs of a rootkit or simply put, it is basically a shell script that makes use of simple linux commands to check for discrepancies in the System binaries. Chkrootkit can easily identify a trojaned system command while it looks for known signatures.
Linux Malware Detect is a free and open source malware scanner for Linux that is designed to use threat data from network intrusion detection systems and create signatures of malware actively being used in attacks.