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