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What is the best way to backup websites that you host on third party hosting site? and what software to recommend?

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Which OS at each end? Solutions will be dependent on that information. – John Gardeniers Jul 27 '09 at 3:17
Probably Linux, but that's something I dont know.. – Graviton Jul 27 '09 at 9:34
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To backup the site, just FTP in and download the data. To backup any database, you'll need to work with the hosting provider to create a backup that you can access. Some do this automatically, others this is a one off request.

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This is pretty similar to this question asked last week.

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