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the adapter (and, perhaps, a more-expensive drive). Macs can boot
from external drives connected to any of these ports.
You can connect a USB 3.0 drive to a Mac that has only USB 2.0
ports; it'll work, but at slower, USB 2.0 speeds. (The reverse is also
true: a USB 2.0 drive attached to a Mac with a USB 3.0 port will
work, but at USB 2.0 speeds.) Similarly, FireWire 400 and FireWire
800 can be mixed and matched; at most, you'll need a cable with a
FireWire 800 connector on one end and FireWire 400 on the other
end. But again, you'll be limited to the speed of the slowest device.
Flexibility: Numerous other devices, such as the AirPort Extreme
Base Station, third-party wireless access points, and NAS devices
(not to mention Windows PCs), have USB 2.0 ports—but usually
not FireWire or eSATA ports—to which you can attach an external
drive. Even though, at present, Time Machine doesn't work with
most such devices, perhaps it will in the future. (If you're not
planning to use Time Machine anyway, it's irrelevant.) And you may
wish to use your backup drive for more than one purpose.
So what's the bottom line?
If you have a Thunderbolt-equipped Mac, a Thunderbolt drive will
give you the best performance. On the other hand, you'll pay extra
for that performance; your options are more limited than with other
interfaces; and frankly, for backups, such high speed isn't that
crucial. Also, be aware that you can buy an adapter that will let you
connect a FireWire 400 or 800 drive to a Mac with a Thunderbolt
port, so if you already have a FireWire drive, that may be an option.
If your Mac has one or more USB 3.0 ports, that's your best bet,
because USB 3.0 drives are extremely fast (even if not quite to
Thunderbolt speeds), more plentiful, and cheaper than Thunderbolt
If your Mac has neither USB 3.0 nor Thunderbolt, look for a drive
with FireWire 800, possibly in combination with USB 2.0 or 3.0.
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