Though Adobe After Effects has a built in Motion Tracking tool which can be used to track simple 2D shots, but the tool has it’s own limitations. To solve complex Motion Tracks, Mocha can be used which is a program entirely dedicated to Motion Tracking and it ships with your copy of After Effects.
Mocha offers wide variety of tools that works in accordance with After Effects. Mocha Motion Tracking data can be exported into After Effects easily which can be later used for Match Move and compositing purpose.
Mocha also has an upgrade known as Mocha Pro which offers additional tools like Removal which you can use to remove or paint out objects from your footage very easily. Mocha Pro is a paid software and you can purchase it from Imagineer Systems.
For Motion Tracking, Mocha or Mocha Pro both serves as a great option.
Here is a great Motion Tracking tutorial by Sasa Jokic where he shows us how to track a footage and Match Move using Mocha and After Effects. A very useful tutorial for understanding basic Visual Effects and Motion Tracking.