One of the most challenging problems in the computational biology is inferring the evolutionary history to construct phylogenetic trees. A phylogenetic tree is a branching topology that represents the evolutionary relationships among groups of organisms. Traditional construction methods of phylogenetic trees rely on building a multiple sequence alignment (MSA) of the corresponding sequences of organisms. However, achieving optimal MSA for a numerous number of sequences is computationally complex. Moreover, even if an optimal MSA is obtained, it may not reflect the evolutionary history of the sequences. So, several free-alignment methods for phylogenetic tree construction have been proposed. In this paper, we investigate a free-alignment construction method to infer the optimal phylogenetic tree based on differential evolution algorithm. The evaluation results confirm that the investigated method succeeds in building the optimal tree with accuracy higher than other considered methods.
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