Performance and accuracy comparison of HAlign4, HAlign3, MAFFT, MUSCLE, and Clustal Omega. (A–C) show scaled SP score, Q score (solid line), TC score (dashed line), and time and memory usage across different sequence lengths. (D–F) display the same metrics across different sequence similarities. Horizontal axes in (A–C) represent sequence length, while in (D–F) they represent sequence similarity. Vertical axes in (A, D) represent scaled SP score, in (B, E) Q and TC scores, and in (C, F) time (s) and memory (MB). Note: For a detailed explanation of the SP score, Q score, and TC score metrics, please refer to Section 3.2.