Which websites ask you to “use the app instead”?
This command-line tool pretends to be a mobile browser (using PhantomJS), and checks whether the website offers to install a mobile app using a couple of heuristics.
For a couple of websites:
$ ./asksforapp http://google.com/ http://facebook.com/
With a list of websites:
$ xargs -L 1 ./asksforapp < alexa/top.txt