Apple Pay, Android Pay and Samsung Pay may seem to have a marketing edge over retailers' mobile wallets, but there is strong momentum among apps that serve individual merchant brands.

One reason for this spike in merchant app development is there is less fear of app fatigue—or consumers storing too many apps on their phones—as smartphone culture matures, said Jon Squire, CEO of Cardfree, a San Francisco company that provides digital marketing and technology to retailers.

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