1. Utilize 2D interaction from RIC-seq and RNAstructure package to predict the secondary structure of SARS-CoV-2 genome RNA

2. Once SHAPE or DMS data are publically available, the predicted structure could be further improved.

3. All the commands are recorded in a shell script named 'run.sh' or 'work.sh' in each folder. Sequentially run scripts in 1, 2, 3a, 3b, 5, and 6 ; Of note, run z2 before 6;

4. The alignment of 429 non-redundant coronavirus genomes, covariance model, and the secondary structure (.ct file) are listed in the folder 'co-variant and structure'