Data sets and example code accompaning the manuscript
Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction
Packages numpy, biopython, and RNAlib from ViennaRNA are required for softconsensus.py. The file provides a class object called Alignment which computes internally the pseudo-energies and proper soft constraints for given alignment and sequence to fold.
For the usage example, we invite users to look at the notebook RNAsoftconsensus.ipynb. Additional package tabulate is needed to disply the MCC table.