Dear Dr. Claudia Romero,

I think Shogun software allows to export motion capture data (3d coordinates of the markers) in c3d file format, however, for kinetic analysis, the software is unable to support equipment such as force platforms (Vicon's support service can clarify this issue: https://www.vicon.com/support).

If the marker kinematic data is sufficient, you can use the "c3d server" application to process a biomechanical model in Matlab:
https://www.c3d.org/c3dapps.html

A software that can be a better option for c3d data processing is Visual 3D Pro (C-Motion). I think the price of this software (~ US$5,000) is lower than Nexus or Vicon BodyBuilder:
http://www2.c-motion.com/index.php

I hope this information is helpful in your project.
Best Regards,