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The Yubikey also supports U2F (the security key standard used by Google and other companies on the web), is a secure store for OTP credentials that are used for two-factor authentication on many web sites (the sort that are issued as a QR code and result in a 6 or 8 digit number) and has a proprietary one time password system used by web sites such as LastPass for two factor authentication. I carry my personal certificate for S/MIME e-mail and my PGP credentials in a Yubikey NEO it is much more convenient for me to use a USB device rather than require smart card readers on all the systems I use.
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For example, you can use most built in smart card readers with a PGP card if you choose to carry PGP credentials in that format. There are other smart cards used in various systems. The latest CACs - perhaps all current CACs - conform to the Personal Identity Verification (PIV FIPS 201) standard. Common Access Card is a smart card issued by the US Department of Defence.
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