select "Check possible repackaging" in Apk Analyzer's detail app report screen
Apk Analyzer sends serialized application detail report to server
Server will add app report to its database
Server compare this app report with reports in database and looks for similar package signed by different certificate - server compares hashes of files in packages to find similar ones, also compare certificate, app version, app install source...
Server answers back to client - App is suspicious / App is OK
This will work like this