What is the differences between alternate CD and desktop CD
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If you are downloading a Ubuntu .iso so you can install Linux, pick the one that is for your type of pc. If it is a 32bit intel or amd use the X86 on some download sites it's called i386 .iso for 64bit use amd64. < You don't have to use the amd64 for a 64bit system the x86 will work fine.
If you are trying to do something else you need to be a bit more specific.
I think "ubuntu desktop" gives you a pretty, graphical install.
"Ubuntu alternate" is a text-mode only install, which is useful if you have difficult or unusual hardware that may not be supported by the "ubuntu Desktop" install.
In addition to allowing a text-mode install the Alternate disc allows for more partitioning options, I think; if I'm not mistaken, it allows you to create and install the system using Logical Volume Management (LVM), which has it's own pros and cons compared to "regular" partitions, and in addition to that encrypted LVM partitioning - in other words, it encrypts the Logical Volumes (or probably the whole Physical Volume in which the Logical Volumes reside) so you can't, at least without great effort and lots of time, get your hands on the data on the disk without knowing the key used in the encryption (actually, the key with which another key was encrypted that was then used to encrypt the disk data).
Though the setup doesn't fill the disk with random data prior to this (probably because that would take a lot of time - possibly full 24 hours for a big disk), so it's clear where the encrypted data begins and ends; some guides (like that of Slackware's) suggest that the portions of disk onto which the encrypted partitions are created are first filled with random data, so that the encrypted data would be "camouflaged" there, making it even more difficult to dig anything up, when it's not even clear where the encrypted parts begin and end.
In short, the Alternate disc offers more options to the installation than the Desktop disc. Though usually Desktop disc is "easier" (or "friendlier") to use, so go for that.