Determining an Ideal MSA Method for Constructing Phylogenetic Tree on DNA Dataset

This study focuses on determining the method for constructing phylogenetic tree from genetic dataset of various species. The genetic tree construction process requires Multiple Sequence Alignment (MSA) to align the genetic dataset. As the size of genetic database grows, MSA has become the bottleneck of the process. The best phylogenetic tree construction needs a good MSA method to align genetic dataset as an advance input. A good MSA method comprises several characteristics such as able to process large dataset, require less processing time and construct accurate aligned sequences. To prove this claim, some experiments were conducted using well-known and available MSA applications (ClustalW, Kalign, MAFFT, MUSCLE and T-Coffee). The resulted aligned sequences were fed into one of the well-known phylogenetic tree construction tool, FastTree. The results showed that MAFFT with locally align and affine gap penalty, MAFFT (E-INS-i) is a good and satisfying alignment tool among the tested aligned sequences to construct the best phylogenetic tree.