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I remember when I jailbroke an iPhone one time I had to use iTunes to restore the default system because there were a lot of applications installed on the phone already (which apparently increases the chances of a brick).

Is this the case with Android phones, specifically the Droid Incredible? I have been using it regularly for a period of two or more weeks and I would like to root it but I want to make sure it is safe to do so with a lot of applications already installed.

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Rooting won't affect any applications that are already installed. All you're doing is giving yourself administrator rights to your phone. You won't have to wipe/reload, etc. unless you plan on installing a custom rom. If you do want to install a custom rom, I highly recommend using Titanium Backup to backup all of your apps and their data. Also do a Nandroid backup (it's like making an image of your phone that you can restore to) right after you root and before you do anything major to your phone (such as installing a rom).

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