Clamav is a universal antivirus, handled both linux and windows partitions.
Terminal
Installing:
sudo apt-get install clamav
At first you have to update the virus definitions with:
sudo freshclam
Then you can scan for viruses.clamscan OPTIONS File/Folder
If necessary start with root permissions:
sudo clamscan
.Examples:
- To check all files on the computer, displaying the name of each file:
clamscan -r /
- To check all files on the computer, but only display infected files and ring a bell when found:
clamscan -r --bell -i /
- To scan all files on the computer but only display infected files when found and have this run in the background:
Note - Display background process's status by running theclamscan -r -i / &
jobs
command. - To check files in the all users home directories:
clamscan -r /home
- To check files in the
USER
home directory and move infected files to another folder:
clamscan -r --move=/home/USER/VIRUS /home/USER
- To check files in the
USER
home directory and remove infected files (WARNING: Files are gone.):
clamscan -r --remove /home/USER
- To see more options:
clamscan --help
Graphical User Interface: ClamTK 
ClamTk is a frontend for ClamAV. You can install it via Terminal with:sudo apt-get install clamtk
You can get the latest version from Bitbucket as Debian package.There is also a PPA (Outdated):
sudo apt-add-repository ppa:landronimirc/clamtk
sudo apt-get update && sudo apt-get install clamtk

Scan Menu: Here you can choose a file, folder or a device for scanning

View Menu:

Quarantine Menu:
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Advanced Menu:

Help Menu: Here you can check for updates.

See:
- ClamTk@Sourceforge
- ClamTk Help
- ClamTk FAQ
From:
http://askubuntu.com/questions/250290/how-do-i-scan-for-viruses-with-clamav
http://www.clamav.net/
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