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I'm trying to implement a cheap backup system using my computer and my friend's computer. The idea is using each other hdd to store a copy of our files through Internet.

Bittorrent Sync would be perfect, but I want to add an extra level of security by encrypting the remote copy, so my friend wouldn't be allowed to see my files, and vice versa. Which app can we use?

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    Truecrypt container would work. – Ramhound Jan 20 '14 at 15:34
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You can use the free client version of CrashPlan for this. With it you can happily create backups on multiple machines with strong encryption of the backups.

CrashPlan works happily through NAT'd routers, is simple to set up and run. It also has the advantage of working across multiple platforms.

The paid version adds secure cloud backups too (make sure you specify your own KEY for real security).

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