A comprehensive systematic literature review of multiple sequence alignment algorithms

Multiple sequence alignment (MSA) is a fundamental technique in computational biology that compares protein, DNA, or RNA sequences to identify regions of similarity reflecting functional, structural, or evolutionary relationships. This systematic literature review examines the diverse land-scape of multiple sequence alignment algorithms, categorizing them based on their underlying approaches and analyzing their strengths, limitations, and applications. We explore seven major categories of alignment methods: dynamic programming, progressive alignment, iterative refinement, Hidden Markov Model-based, consistency-based, structure-based, and machine learning-based approaches. Through comprehensive analysis of recent benchmarks and literature, we identify key innovations, performance characteristics, and emerging trends in the field. This review provides a detailed overview of the evolution of multiple sequence alignment algorithms and their applications in modern bioinformatics.