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RNApyro You only need the python script src/RNAPyro.py The arguments are as follows: Required: -f <file_path> Path to the file containing the reference sequence, the MSE (optional) and the secondary structure. The FIRST sequence in the file will be used as reference -m <int> The numbers of mutants required -a <float> The weight given to match the MSE or the secondary structure, between [0,1]. A weight of 1 will only take into account the secondary structure, 0 only the MSE Optional: -p <float> The penality for a non canonical base pair (default sys.maxint) -b <int> Backtrack stochastic, number of sequences to output -no_profile Do no output the resultant profile