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Can I exclude airlines or filter flights by non-stops?

Yes, you totally can.

Hopper now includes the option to apply filters for your flight watches in both iOS and Android.

After you search your origin and destination in the Hopper app, simply tap the button that says "Filters" above the color-coded calendar on the following screen. You can then select the filters you would like to apply: removing basic fares and low-cost carriers, non-stops only, or shortest layovers. Your pick!