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Scan Website domain to verify no virus malware links

How can a website be scanned to determine if there are any links on the website that may have been hacked or have hidden hacks.

There is a local website that is used by agencies for local training purposes,   the web master of the site states nothing is wrong with the site although randomly users  from our organization are getting virus threats from the local workstation antivirus software.  The threats are real as one was the crypto threat.   The AV is catching the threats which seem to be happening when the user visits that particular site.  

How can I check or scan that site to verify links are safe and doesn't have any hidden hacks?   We do have a webfilter and when I check the filter after the threat is found ,  it shows the workstation was accessing an off the wall url in-addition to the original website .  I block the url but it seems to change.
VulnerabilitiesNetwork SecurityWeb Servers

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Wesley Miller
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Thank you for your information.   I did run the online scans on the website and it came up without threats.    I will still pursue  investigating this site as I am still concerned that users are getting real  threats showing up through the AV randomly for the site.
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Thanks for sharing.
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Wesley Miller
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You can do a website download with HTTrack ,
As it mirrors the website onto your hard drive,  your Anti Virus should inform you of any malware it sees during the mirror.
Once the mirror is finished you can then  scan the folder for any malware to ensure it has nothing your scanner might have missed during the download.

See: http://www.httrack.com/
Web Servers
Web Servers

A web server refers to the software that helps to deliver web content that can be accessed either through the Internet or through an intranet. The primary function of a web server is to store, process and deliver web pages to clients. The communication between client and server takes place using the Hypertext Transfer Protocol (HTTP). The most common use of web servers is to host websites, but there are other uses such as gaming, data storage, running enterprise applications, handling email, FTP, etc.

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