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The construction of phylogenetic trees is an NP-hard problem because the number of possible trees increases exponentially with the number of DNA or protein sequences included in the analysis. The large amount of data and the task's complexity means that phylogenetic trees can't be interred without computational help. Since the 1960s, researchers have published numerous studies addressing the problems of molecular phylogenetic analysis methods in theory and practice. Other studies have refined the methods and evolutionary models over time, but challenges still remain. The cited references in this review represent only a few examples from a vast amount of literature.