Computer-implemented methods for analyzing computer programs written in semi-structured languages are disclosed. The method is based on unification of the two classic forms of program flow analysis, control flow and data flow analysis. As such, it is capable of substantially increased precision, which increases the effectiveness of applications such as automated parallelization and software testing. Certain implementations of the method are based on a process of converting source code to a decision graph and transforming that into one or more alpha graphs which support various applications in software development. The method is designed for a wide variety of digital processing platforms, including highly parallel machines. The method may also be adapted to the analysis of (semi-structured) flows in other contexts including water systems and electrical grids.