How to do a php trace

I know there are modules to trace through the database tables effected when you browse your Drupal site. How would you do a step/trace through the php code of Drupal? I'm primarily a Microsoft Visual Studio studio user, so I'm comfortable with debuggers and IDEs. Would I use Eclipse or Apatana? This is not a support issue. I want to figure out the inner workings of Drupal. Thanks in advance.