Goal: Prototype script to predict pseudoknots in rna structures.

How to run: You can execute the program through the use of a few scripts.

(1) run_ht.sh -- running MH on a single sequence file Usage: run_ht.sh [-r] sequencefile.fa[sta] -r : tells script to rerun SFold, if this is not designated MH will grab the SFold output from the last time SFold was run

(2) sampling.sh -- running a set of sequence files at once Usage: sampling.sh grabs all fasta files (*.fa) from the input_files directory, runs MH on each 5 times and outputs to a file with the name of the sequence to the output_files directory