The algorithm used for the one time password in the Google Authenticator app is known as the Time-based One-Time Password (TOTP) algorithm. The TOTP algorithm is a standard algorithm approved by the IETF in (RFC 6238) totp-rfc.
It is a little known fact that you can use the TOTP algorithm to secure your user accounts in Linux systems. This article will walk you through the steps necessary. While the exact commands will be for Fedora 20, the TOTP algorithm can be deployed to any Linux distro with a little modification.
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