AGGREGATES is a Fortran code developed to find and analyze molecular structures in computer-simulated trajectories. The program can read trajectory files from several MD packages namely, DLPOLY, CHARMM, LAMMPS, and GROMACS. Additionally, PDB files can also be used. The program output consists of a series of statistical functions that can be used to characterize the size, shape, and organization of molecules in a network. An extensive description of the program functionalities can be found in the following publication: C.E.S. Bernardes; J. Comp. Chem. 2017, 38, 753-755. (http://dx.doi.org/10.1002/jcc.24735) This work was supported by Fundação para a Ciência e a Tecnologia (FCT), Portugal: UIDP/00100/2020, with DOI 10.54499/UIDP/00100/2020 (https://doi.org/10.54499/UIDP/00100/2020). UIDB/00100/2020, with DOI 10.54499/UIDB/00100/2020 (https://doi.org/10.54499/UIDB/00100/2020 LA/P/0056/2020, with DOI 10.54499/LA/P/0056/2020 (https://doi.org/10.54499/LA/P/0056/2020) 2021.03239.CEECIND/CP1650/CT0003, with DOI 10.54499/2021.03239.CEECIND/CP1650/CT0003 (https://doi.org/10.54499/2021.03239.CEECIND/CP1650/CT0003).