Clamav is a free anti virus software which is able to detect many types of malicious software, including viruses on the servers. One of its main uses is on mail servers as a server-side email virus scanner. Below is some useful clamav commands.
clamscan -r path-to-dir
It will scan directories all directories and sub directories recursively..
clamav -ril /home/user/clamav.log
It will scan the user home directory and output the results to the specified file.
-i option is used to report only the infected files.
clamscan -ir / -l cscanreport
It will scan the entire server (/) and will create an output file cscanreport in the present directory.