This study aimed to develop a toolbox for kinematic and dynamic modeling and analysis of the high degree-of-freedom (DOF), redundant serial robots used widely in cooperative and space applications. With the Advanced Robotics Analysis Toolbox (ARAT), kinematic and dynamic modeling and analysis of the complex, high DOF, serial robots which may have universal, spherical, prismatic, or rotational joints with more than one DOF and a mobile or stationary base can be easily accomplished. The ARAT was used to design and analyze different complex structures of serial robots for robotic education students and robotics researchers who design and build exceptional new robots. The robot's kinematic and dynamic parameters including link lengths, directions, masses and inertias can be entered into the ARAT using a user-friendly interface. Solid models of the robots can be created in a three dimensional (3D) environment for virtual reality simulations. In the ARAT, forward and inverse kinematic models, Jacobian matrix, trajectory planning, forward and inverse dynamic models can be produced in a computationally efficient way. All of the physical robot parameters such as angular and linear velocities, accelerations, forces, and torques at the joints, link origins and the center of mass of the links can be computed in 3D. The ARAT includes support for the most commonly used trajectory algorithms in serial robots, including polynomial, trigonometric (harmonic, cycloidal, elliptic), exponential, Gaussian, and Fourier-based (Gutman, Freudenstein). These trajectories can be applied easily to each joint of the robots. To compare the kinematic and dynamic results obtained from ARAT and MATLAB-Simscape Multibody simulation program, different structures of the serial robots were simulated in both programs. The results that produced from ARAT and MATLAB-Simscape were similar. The ARAT is much better from the serial robot simulation toolboxes existing in literature in terms of computation capability, visual ability, and easy usage.