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Drive-by malware has become a huge problem lately. That’s where hackers use a vulnerability in your web site to embed malware within it. Then, anyone who visits your site will download the malware onto their computers.

That’s why Redwood Shores, Calif.-based Qualys is launching two new services today. The first one is Qualys Guard Malware Detection, a free cloud-based service that scans your site to determine if you’re a victim of a drive by and your site has inadvertantly become a distributor of malware. The software also cleans up the malware and provides you with automated alerts. It identifies the snippets of bad code so that you can immediately remove it.

The second is Go Secure, a paid service that lets companies take more actions to protect themselves. For $995 a year, the service checks to see if your web certificate is up to date, which allows for secure e-commerce. It also scans for other vulnerabilities and reviews your web applications for vulnerabilities. If you subscribe and pass muster, you get a security seal on your site. If your site is hit with an attack, the security badge is removed and then automatically reinstated when the site is cleaned up.

Qualys was originally founded in 1999 to pioneer a software-as-a-service model for security software. The Qualys Guard service is used by 4,000 companies.Qualys itself now has $57 million in revenues and 42 percent of Fortune 100 companies are using its security software. The company has 240 employees and has raised $65 million to date.

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Philippe Courtot, chief executive and chairman, said in an interview that the software is highly accurate, with only 3.2 errors for every 1 million scans. It can also scan millions of URLs daily. Courtot said there are built-in protections to make sure that the scanning does not slow down a site so it is unresponsive.

The software uses both static analysis and behavioral analysis to identify malware while scanning. The static analysis identifies the source code that is typically used in malicious attacks, such as encoded JavaScript, web bugs, and character encoding inside of inline frames. Behavioral analysis catches behavior that occurs when visiting a site with an unpatched browser or operating system. It monitors the unpatched machine for suspicious behavior, such as programs being installed or files being written to a hard disk.

Rivals include Dasient.

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