How can Sequence Alignment Method Affect the Phylogenetic Relationship Results?

Abstract

Sequence alignment is a fundamental step before analysing the phylogenetic relationships between organisms. The effect of the alignment method on the phylogenetic relationship results has not been well studied. Three methods for sequence alignment are available in Geneious software: (1) Geneious alignment, (2) ClustalW, and (3) MUSCLE. The study aimed to investigate the impacts of these three alignment methods on the phylogenetic relationships between test organisms. Therefore, the phylogenetic tree was established for the same organisms (honey bee species and subspecies) 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 relationship between the closely related organisms. Based on this study, it is better for researchers to test different alignment methods before constructing the final phylogenetic tree to select the most suitable one.

Keywords

• bioinformatics
• software
• geneious
• ncbi
• genetics