Is it a good idea to use Drake for motion capture problems

I'm searching for a toolbox that will aid in the development of a trajectory optimisation method to perform pose estimation/motion capture of quadruped animals. I have data from multiple cameras and would like to fit a skeletal model to the data. I'm using trajectory optimisation to obtain the pose and dynamics (internal torques and external contact forces) of the animal during locomotion.

I have a solution using custom software -- but it is very slow and hinders the experimentation process.

Would you recommend using Drake for this? If yes, which modules do you recommend I take a look at? If not, what are the drawbacks of trying to use Drake and do you recommend any other software for this?

To make sure I understand, it sounds like you have a model that you like (kinematics + dynamics parameters are fixed), and you have the position trajectories of, for instance, a handful of markers, and you want to recover the torques and ground reaction forces? And you're thinking of using trajectory optimization with a cost on e.g. matching the positions of the markers over time.

The choice of trajectory optimization codes can change somewhat significantly depending on whether you know which bodies are in contact on each frame or whether you are trying to infer that. For the cases of known contact sequences, you might look at this example or try out the slightly more general hybrid multibody code which should land soon.

If you're inferring the mode sequence then you might want something like https://groups.csail.mit.edu/robotics-center/public_papers/Posa13.pdf or iterative LQR through contact -- people have definitely implemented those in Drake but we don't have a shiny implementation in Drake's main repo yet.

There are some more general notes about these algorithms here.