ZAP Attack Proxy – open source software to detect vulnerability.
Disable PHP insecure functions with disable_functions
Find IP with Most Access from Apache Log
Monitor file changes in your Website
inotifywait
Stop xmlrpc.php attack on Cpanel Server
Stop SSH bruteforce with endlessh
https://suricata.io
Check for hacker files
find ./ -name '*.php' -exec grep 'Spy Shell' {} \; -print
find ./ -name '*.php' -exec grep 'system(' {} \; -print
find ./ -name '*.php' -exec grep 'exec(' {} \; -print
find ./ -name '*.php' -exec grep 'passthru(' {} \; -print
Disable PHP Files on Upload folder
deny from all