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