Nessus is a great security audit tool, and it works quite well with Ubuntu. But, if you install Nessus from the Ubuntu repositories, you're going to be stuck with an older version. If you need the better functionality of the newest version, you'll need to download it from the Nessus.org website. To complicate matters a bit more, there's a 64-bit version of the Nessus server, but there's only a 32-bit version of the Nessus client. So, if you're running a 64-bit version of Ubuntu, you'll need to work a bit of magic to get everything to work properly