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Molecular shape is one of the most critical factors that determine molecular function. To properly understand the function of a molecule, it is necessary to explore its geometric properties more effectively and efficiently in addition to its physicochemical properties. Due to the complexity of the problems in biomolecular structure, in-silico approach is inevitable for many cases and is becoming more popular. In this paper, we introduce BetaMol, a comprehensive, powerful graphics-based software for molecular modeling, analysis, and visualization. BetaMol is based on the recent theory of the beta-complex which is derived from the Voronoi diagram of spheres. The entire set of powerful features of BetaMol is completely based on a single framework of the mathematically rigorous and computationally efficient theory of beta-complex. BetaMol is implemented in the standard C++ language with the OpenGL graphics library on Windows platform. Both BetaMol and some of its important functions ported for Linux platform are freely available at Voronoi Diagram Research Center website (http://voronoi.hanyang.ac.kr).