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Secure file transfer allows you to transfer files over a secure connection, that is, one that is encrypted and in which the identity of the remote machine (the computer you're connecting to) has been validated. One common use for secure file transfer is for backing up your work on your computer to the server for safekeeping. Another use might be for retrieving files from the server while you're working from your computer at home.
The Linux command line interface offers two methods of secure file transfer: secure copy (SCP) and SSH file transfer (SFTP). Both technologies are based on secure connections provided by SSH.