A new version of PETOOL (Parabolic Equation Toolbox) is introduced with various additional capabilities. PETOOL is an open-source and MATLAB-based software tool with a user-friendly graphical user interface (GUI) for the analysis and visualization of electromagnetic wave propagation over variable terrain and through arbitrary atmosphere. Four novel features of the second version are as follows: (i) Several evaporation duct models have been developed. (ii) Real atmosphere data have been included in the form of "Binary Universal Form for Representation (BUFR)" data developed by "World Meteorological Organization (WMO)". (iii) Real terrain data have been incorporated into the toolbox in the form of "Digital Terrain Elevation Data (DTED)" developed by "National Imagery and Mapping Agency (NIMA)". (iv) A special add-on has been developed to generate a 3D coverage map of propagation factor/loss on real terrain data. The toolbox can be used for research and/or educational purposes to analyze more realistic propagation scenarios in an easier and flexible manner.