The program requests two input files:
1. Sequence alignment file. The alignment file should be prepared in FASTA format, e.g., the first line contains sample name and the second line contains nucleotide sequence (without line breaks).

Example of input file file:

2. Secondary intructure information file. Information on position of stems and loops should be given as columns: the fist line contains information on numbers of paired nucleotides in stems and loop, the positions of paired nucleotides in stems are started from the second line as two numbers per line, and then the positions of nucleotides in loops as one number per line.

Example of input file: