blindgaenger

One of the main reasons for switching to Linux was a rootkit hitting my Windows installation. This was the best time to play with Ubuntu (before reinstalling Windows again, as I thought). I stayed, but since then I run these commands regularly. :)

Rootkit Hunter

Although this shouldn't be the main reason to use it, but Rootkit Hunter has a very good command line interface. Your shell should support colors to enjoy it!

sudo apt-get install rkhunter
sudo rkhunter --versioncheck
sudo rkhunter --update --propupd
sudo rkhunter --check

chkrootkit

Actually chkrootkit seems to check the same stuff as rkhunter. But the downside is the missing update command.

sudo apt-get install chkrootkit
sudo chkrootkit -V
sudo chkrootkit

Clam AntiVirus

Get new virus definitions with freshclam . But apt-get should have installed an update-deamon in /etc/init.d/clamav-freshclam, so this shouldn't be necessary.

sudo freshclam 
sudo clamscan --recursive --quiet --bell --stdout /home >/tmp/clamscan.log
less /tmp/clamscan.log

Yep, there are GUIs for clamav out there. Then try clamtk if you need one.