"Algebras/MFE/alg_mfe.gap" evaluates the free energy of a candidate and selects the minimal one from. It uses a GAP internal interface to the Vienna energy values, which are provided by the Turner Group. By default, these values are hard coded but can be replaced with a file, provided via the parameter -P. Default temperature is 37 °C, but can be changes via parameter -T, as in the Vienna-Package.

Since some algebra functions are commonly used by other algebras (Algebras/MFE/alg_outside_mfe.gap and Algebras/MFE/alg_pknot_mfe.gap), they are outsourced in the files Algebras/MFE/algpart_mfe_basic.gap.