Is there a way to install antivirus software on my server or at least in the sites files, to clean up the website that is infecting viewers computers? It infected my computer when I checked into it after a complaint. The site has hundreds of pages. The person informing me of the problem said he got a js virus warning message. I don't get a message when I view the site. I have disabled the site for now. Any input would be appreciated.
Your problem will not be resolved by scanning your site with an antivirus tool. If you are lucky enough to find and remove the file, you still have the problem that people are able to put such files on your server. Or, they are able to edit your pages so that they pull content from other locations. In either case, you have a responsibility to review each and every page and each and every directory on your server and make sure that it is clean. Then, you need to fix all security holes and harden all scripts so that you prevent people from uploading content and/or rewriting files. If you are using third party scripts, you need to make sure you are at the latest patch level. If the script is no longer being worked on, you need to find a secure replacement.