Alignment 1 Bioinformatics 1 Co-variations 1 Covariation 1 Energy minimization 1 Forecasting 1 Free energy 1 MFE 1 Minimum free energies 1 Muscle 1 Pseudo-knots 1 Pseudoknot RNA 1 RNA secondary structure 1 RNA secondary structures 1 RNA sequence 1 RNA sequences 1 Secondary structures 1 Sequence alignment 1 Sequence alignments 1 Thermodynamic energy 1 Thermodynamic energy minimization 1 article 1 controlled study 1 muscle 1 noise 1 protein secondary structure 1 sequence alignment 1