I will be a bit more descriptive to flush out my questions better. I have two "rods" in three space. One rod is fixed, while the other is not. I need to apply a torque to the unfixed rod to make it become parallel to the fixed rod.
Okay, I am able to get the rotation matrix from each of the "rods", is there any way to "subtract" them to get the matrix rotation that separates them, because then I could use what you said. Also how would I go about calculating the eigenvalue of a rotation matrix. (I am not used to rotation matrices which is why I was using angular velocity above. After making this reply I will be looking up eigenvalue on google in case you don't want to go into that)
