Path-based encodings are in proximity of each other except for Daylight, which is linked to PubChem and FCFP, and RDKIT, which is only connected to Avalon. DFS is the fingerprint of this category that is most correlated within its category, reaching all other path-based algorithms in at most two steps within the MST. Circular and string-based fingerprints are mostly interconnected with each other, apart from LSTAR. MHFP connects with FCFP, ECFP and RAD2D, consistently with the fact that it also relies on circular fragments, while MAP4 connects with ASP, which likely reflects the fact that it encodes topological distances between atom pairs. FCFP is unique among all fingerprints, given that it connects with a fingerprint from all other categories except for pharmacophore-based encodings. This is especially surprising given that FCFP uses pharmacophoric information for the atom identifiers, which one might assume would lead to higher correlation with PH2 and PH3. Furthermore, it is notable that ECFP and FCFP correlate more strongly with MHFP than with each other, despite using the same algorithm except for the atom definitions. This seems to suggest that MinHashing SMILES substrings provide a hybrid representation that captures both chemical and pharmacophoric properties of the molecule.