To create a 3D model of human shoulder, you can use 3D scanners machine and then export to the digital simulation and modeling software to calculate and analyze. Par example, use ABAQUS sortware to simultaion and modelling...
Well, depends upon what kind of analysis you would like to do. Is it stress analysis, cfd or thermal etc? Depending upon kind of simulation, you can go for conventional softwares like MatLab, ANSYS but you can also give a try to CAD/CAM softwares like Solidworks, Rhinoceros, Catia etc.