To run the Monte Carlo simulations, type the following command and the parameters’ value at the terminal:

java resistanceSim [Duals = 1 | Doubles = 2 | Duals & Doubles = 3] [Segment] [HF] [Runs] [Hits]

[Duals = 1 | Doubles = 2 | Duals & Doubles = 3] : specify whether the target graph consists of effective Duals only, effective Doubles only, or both.
[Segment] : specify the segment targeted in a Dual only graph; this is applicable when Duals option is specified.
[HF] : hedge-factor of the target graph. When Duals & Doubles option is selected, HF is set as 6 in the simulations.
[Runs] : number of independent viruses
[Hits] : minimum number of mutations in each viral target sequence needed to become resistance