Phylogenetic analysis is a fundamental concept in computational biology, which helps in understanding evolutionary relationships, species divergence, and functional conservation based on biological sequence data. In general, phylogenetic analysis involves a number of sequential steps, such as sequence collection, multiple sequence alignment, model selection, phylogenetic tree construction, and statistical validation, which are usually carried out using different software tools with heterogeneous workflows. In this work, we propose a Python-based phylogenetic analysis pipeline, which integrates a number of important steps in phylogenetic analysis into a unified framework. The proposed system incorporates a number of popular sequence alignment algorithms, such as Multiple Alignment using Fast Fourier Transform (MAFFT), Multiple Sequence Comparison by Log-Expectation (MUSCLE), and ClustalW, as well as different phylogenetic tree reconstruction approaches, such as Neighbor-Joining (NJ), Unweighted Pair Group Method with Arithmetic Mean (UPGMA), Maximum Likelihood (ML), and Maximum Parsimony (MP). In addition, tree visualization, as well as comparative assessment using topological distance measures and statistical hypothesis tests, is performed in the proposed system, which includes Robinson-Foulds (RF), Approximately Unbiased (AU), Kishino-Hasegawa (KH), and Shimodaira-Hasegawa (SH). The results obtained from the analysis of the datasets demonstrate that the combination of the MAFFT-based alignment methods with the Maximum Likelihood tree reconstruction strategy results in the generation of trees with high statistical support according to the tests used for the analysis.
Gambhava et al. (Thu,) studied this question.