How can sequence alignment method affect the phylogenetic results?

Hossam Abou-Shaara


Sequence alignment is a necessarily step before analysing the phylogenetic relationships between organisms. The effect of the alignment method on the phylogenetic results has not been well studied. In Geneious software, the alignment can be performed using different methods including Geneious alignment, ClustalW, and MUSCLE. In this study, the phylogenetic tree was established for the same organisms after using the three alignment methods, and then the results were compared. The constructed tree after using ClustalW differed than Geneious alignment and MUSCLE without a clear effect on the closely related organisms. Based on this study, it is better for researchers to test different alignment methods to select the most suitable one.


bioinformatics; software; Geneious; NCBI; genetics

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