Why does the Arduino Due have a native and USB programming port?

Question

According to the schematics, the Arduino Due has two USB inputs:

1. Native
2. Programming

Why is this? And when would I use the different ports?

Answer 1

Either port can be used for programming, but the native USB port lets you do other things:

It also enables the Due to emulate a USB mouse or keyboard to an attached computer. To use these features, see the Mouse and Keyboard library reference pages.

The Native USB port can also act as a USB host for connected peripherals such as mice, keyboards, and smartphones. To use these features, see the USBHost reference pages. _{http://arduino.cc/en/Main/arduinoBoardDue}

So you can use the Due to interface with USB devices or connect it to your computer and have it act like a USB device.