When you think of animating a skeleton, or the body containing it for that matter, it should be obvious that the movement is generated at the beginning of the relevant limb or body part and is then propagated from there. If a leg is moved in a walking motion, for example, the movement starts in the thighs and hips, as the muscles there work to lift up the leg. The lower leg and foot muscles then coordinate to keep themselves oriented properly so that they can be placed on the ground again.
There are two ways of animating this, each with its own set of advantages and disadvantages.
The first method is to specify the end condition of the foot being moved from position A to position B, and then calculate from there how you can accomplish this movement using the available joints in the skeleton. This is referred to as Inverse Kinematics (IK for short). While it's easy to specify what has to happen, a lot of the magic then has to be solved by algorithms, which can take...