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Aligning multiple biological sequences such as protein sequences or DNA/RNA sequences is a fundamental task in bioinformatics and sequence analysis. Studying these alignments provides scientists with information needed to predict the sequences’ structures, determine the evolutionary relationships between them, or discover drug-like compounds that can bind to the sequences. Unfortunately, multiple sequence alignment (MSA) is NP-complete. In addition, the lack of a reliable scoring method makes it harder to align the sequences reliably and to evaluate the alignment outcomes.