MuLiMs-MCoMPAs software is for the calculation of 3D bio macromolecular (protein and peptide) descriptors based on the two-linear and three-linear algebraic forms. It is thus the unique software that computes these kinds of indices, establishing relations among two and three aminoacids and applying several (dis)similarity metrics or multi-metrics, matrix transformations (simple-stochastic and mutual probability), cut-offs, local calculations and aggregation operators. This software was developed in Java programming language, and it uses the Chemical Development Kit (CDK) library for the manipulation of the chemical structures and the calculation of atomic properties. This software is composed by a desktop user-friendly interface and an API library. The former was created to ease to the users the configuration of the different options of the bio macromolecular descriptors, while the library was designed to be easily integrated in other software for bioinformatics applications