Specialized software is pervasive in all aspects of music research, teaching, composition, and performance. We include a few open educational resources here, namely metaScore, which allows users to create open, interactive textbooks, and the archived (alas) JPMorganChase KIDS Digital Movement and Sound project, which was designed to initiate children into the creative process. Most of the remaining projects cluster in what has variously been called systematic, empirical, digital, or computational musicology, which is to say highly interdisciplinary, data oriented research practices that try to understand music by considering multiple aspects. Related sub-disciplinary offshoots include music signal processing, music information retrieval, music psychology, musical acoustics, analytical ethnomusicology, and music archaeology, among others. Some software applications tackle common processing tasks needed for empirical work. Aruspix, for example, is a desktop application for optical music recognition (OMR) that is specialized for early typographic music prints from the 16th and 17th centuries. Other applications assume the presence of a finalized, high quality dataset that you want to analyze (e.g., music21, jSymbolic) or present online (Enhancing Music Notation Addressability, Verovio).
In no particular order…