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custom recovery is a third-party recovery environment. Flashing this recovery environment onto your device replaces the default, stock recovery environment with a third-party, customized recovery environment. This is a bit like flashing a custom ROM like CyanogenMod - but, instead of replacing your device's Android operating system, it replaces the recovery environment.
A custom recovery environment will do the same things as the stock Android recovery. However, it will also have additional features. Custom recoveries often have the ability to create and restore device backups. Custom recoveries allow you to install custom ROMs. ClockworkMod even offers a "ROM Manager" app that allows you to access many of these features from a running Android system - this app requires a custom recovery installed to function.
*Popular Custom Recoveries*
ClockworkMod Recovery (CWM) can create and restore NANDroid backups - backups of an Android device's entire file system. ClockworkMod offers a ROM manager with a file browser that allows you to easily browse for and install custom ROMs via ClockworkMod Recovery and manage and restore backups. It also has other advanced features that will be useful if you're installing and dealing with custom ROMs.
Team Win Recovery Project (TWRP) is a touch-based recovery environment. Unlike other recovery environments - including Android's default stock recovery, which needs to be controlled with the device's volume and power buttons - this recovery environment has a touch-based interface you can use by tapping your fingers on on-screen buttons. TWRP even supports themes. Like CWM, TWRP offers ROM installation and backup features the stock recovery environment doesn't.
CWM and TWRP are the two most popular custom recoveries, but other custom recoveries may be available for some devices.
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