Since the analysis of transmission aims for the reconstruction of relations between sources, it focuses on the differences of rather similar items. Therefore, it is necessary to find substitution models which are optimized for distinguishing fine levels of differences and to deal with the structural ambiguities and visual variance of mensural notation. This book reports on the task of developing concepts for a computational analysis of the transmission of mensural music based on concepts of phylogenetic analysis. Part one lays the theoretical foundations, wrapping the key assumptions of stemmatics for 15th and 16th century mensural music and the computational methods of phylogenetic analysis. Part two covers in a case study the methodological and domain-specific requirements of mensural music, follows main questions of encoding and sequence-building up to an approach utilizing surrogate data analysis to determine the most suitable substitution model for a comparison of sources.