As much for you as for myself, here is a list of tools you might want to have in mind :
Software you can install to avoid issues
ClamAv (Antivirus)
chkrootkit (Check for Root kits)
Maldet or LMD (Linux Malware Detection)
Ispprotect (commercial 90$ a year)
Commands you can run to check for issues
netstat –an
Displays the network connections and generic statistics
ps –ef
Lists every currently running process
top n 1 b
Displays running processes, their owners, how much memory each process is using, and how long the processes have been running. It also includes system information, such as uptime, number of users, memory usage, and the number of active tasks.
dmesg
Outputs all kernel messages currently in the ring buffer
who
Prints information on all current logged in users
last
Lists all users who logged in or out since a file was created. By default, the file is /var/log/wtmp
lsof
Lists information about open files and can indicate which process is used it