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Is there a way to add the Apple File Protocol (AFP) to Windows Server for shares, currently Windows uses SMB but the transfer rate to OSX clients is ridiculously slow, I am currently running an Ubuntu server box with AFP but would like to know if there is an option or way to get it working on Windows Server (2008 R2).

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Interestingly, the next release of OS X is switching to smb2 instead of AFP for sharing between Macs. – Alan Shutko Sep 5 '13 at 21:34

Microsoft used to include Services for Macintosh, but it's no longer supported in Server 2008, so you'll have to go for a third party solution.

There's no Windows port of netatalk, but you could of course run it virtualized. Otherwise, the only options appear to be the commercial products MacServerIP and ExtremeZ-IP. Unfortunately ExtremeZ-IP is quite expensive, at $795 for a 3 client license. MacServerIP has no listed price that I could find, which suggest it's also priced rather highly.

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