Epistasis/synergy analysis

Epistasis/synergy analysis tool: it first selects the top-N single mutations ranked by the chosen effect direction, then runs the epistatic siamese network on all pairs of these positions, comparing the actual double-mutation ddG with the sum of the two single ddGs to identify synergistic and antagonistic mutation combinations.

The output includes, for each position pair, the single ddGs, additive ddG, epistatic ddG, synergy value (synergy = epistatic - additive) and interaction type. A negative synergy (stabilizing direction) or a positive synergy (destabilizing direction) is marked as synergistic.