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How to white list my applications

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I need a solution

We develop software which will upload the files to a website. We are facing the false positive error from different antivirus vendors.

We have update file, downloader exe(which download the files from web) and full setup ( which includes update files). We will release the update as soon as there is any change in the website schema to which we are uploading files.

When the customers run the update file or install a new setup they will get warning from antivirus vendors like Symantec, Norton that very less people have used this setup (less than 5) and last week Norton and Symantec deleted the our setup by giving warning “WS.Reputation.1”.

I used to scan in virus total before releasing but there I don’t get any virus warnings there.

I know I can white list my files before uploading to my server, but have a problem with that.

As I said our software is used to upload files to website, as soon as there is any change in that website I have to release the new update. But white listing will take certain time to upload the latest definitions to antivirus vendor’s servers and customers have to download that before running my setup in order to get rid of false positive. So I think white listing will not completely solve my problem.

I know about false positive report  to symantec, but that is one after detecting the problem. I think prevention is better than cure.

What things I can do to overcome this problem?

Is there any way to keep history of my exe version with antivirus vendors so that they can trust my file?

Also how big software companies overcome antivirus false positive problem ?

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