How to create an inverted PWM on the Due via software Hello I am i need of a piece of code that lets me invert a PWM signal of two PWM pins on the due. Example D1 will be 101010 and D2 will be 010101. Is it possible?

Im pretty limited in my options because, doing it externally is not an option because there will be a time where a change in mode is needed and both pins will be sending signal independently. Manually pulling the pins High and Low is also not an option for me because this will make the code blocking other codes.
Not using the Arduino API, no. But you can by direct manipulation of the SAM3X8E registers.

You should study section 38 of the datasheet, where it mentions in the list of facilities:


  
  Independent Complementary Outputs with 12-bit Dead-Time Generator (Also Called Dead-Band or Non-Overlapping Time) for Each Channel