Nessus is one of the most famous vulnerabilityscanners, here's an extract from their site:
The Nessus® vulnerability scanner is the world-leader in active scanners,
featuring high-speed discovery, configuration auditing, asset profiling,
sensitive data discovery and vulnerability analysis of your security posture.
Nessus scanners can be distributed throughout an entire enterprise, inside DMZs
and across physically separate networks.
Installation
First, you'll have to download nessus and his plugins
sudo apt-get install nessusd nessus nessus-plugins
Now we're gonna make nessus run defaultly
sudo ln -s /etc/init.d/nessusd /etc/rc2.d/S20nessusd
Now we're going to startup nessus
/etc/init.d/nessusd start
Now we're going to add a user
sudo nessus-adduser
And to be able to scan any host, you just add "default-accept"
Now we'll restart nessus
/etc/init.d/nessud restart
and now we startup nessus
sudo nessus
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