Comparative analysis of some multiple sequence alignment tools using Gallus gallus COX1 sequences

Multiple Sequence Alignment (MSA) is an essential method in bioinformatics for detecting conserved sequence regions and deducing evolutionary relationships. However, performance variability exists among MSA tools, and different tools yield varying results depending on the dataset. This study conducts a comparative evaluation of four widely used MSA tools: ClustalW, Clustal Omega, MUSCLE, and MAFFT. The alignment quality and processing efficiency of these tools were assessed using 40 randomly selected Gallus gallus cytochrome c oxidase subunit 1 (COX1) DNA sequences. The findings offer valuable insights into the specific contexts in which these tools may be most effective. MAFFT demonstrated a notable advantage in processing speed, while Clustal Omega and MAFFT excelled in Column Score (CS). For Total Consensus (TC) score, ClustalW and MUSCLE showed superior performance, and Clustal Omega exhibited the highest performance based on Root Mean Square Deviation (RMSD) values. No significant difference was observed between the tools in terms of the Sum-of-Pairs (SP) score. This study serves as a valuable resource for researchers seeking to optimize the use of MSA tools for their specific applications.