read_me

#bpRNA-align scripts
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#bpRNA_align.py: This script takes two inputs and has multiple flag options and one output. The output consists of a file where each line contains the alignment information of one pair. input 1) -f, a list of files in either "st" format or "dbn" format. input 2) -w the bandwidth, which is typically set to 1/8 - 1/4 the length of the longest sequence. flag options include -a (to include alignments in the output file), -p (plot M, X, and Y matrices for the aligned structures), -o (specify the name of the output file)
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#bpRNA_align_module.py: This module performs the aligning task, once the files are processed and the key information is retreived. This module includes the gap penalties and the substitution matrix for scoring. 
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#an example run file is available, "run_bpRNA_align.sh", and can be run using the following command: "bash run_bpRNA_align.sh"