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I went to their store, and it appears to be an USB stick (yeah like I have a spare USB port), so I don't get your comment - why _wouldn't_ it work the same way all other programs do?

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Because it works by emulating an USB keyboard and keystrokes (which is pretty ingenious idea imo).

"The Key generates and sends unique time-variant authentication codes by emulating keystrokes through the standard keyboard interface. "

The yubikey pretends to be a USB keyboard to input the auth token, so if you have the keyboard re-mapped in software it will mess up the auth token.

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