The overall workflow consists of three main steps: (A) the first step is to build the Burrows–Wheeler Transform (BWT) index of the center sequence, which serves as the reference for alignment. The second step involves pairwise alignment of the central sequence with each input sequence using the BWT index. Exact matches are identified, and the longest pair-matches set is found. The third step combines the pairwise alignments to generate the final multiple sequence alignment (MSA). (B) The detailed process of pairwise alignment includes constructing the BWT index for the central sequence (sequence 3), inputting the suffix of another sequence (sequence 1) to find exact matches using the BWT index, and identifying the longest set of pair-matches between the central sequence and the query sequence. For unaligned segments, the wavefront alignment algorithm is used to perform pairwise alignment, enhancing the alignment of long sequences. Finally, the aligned segments are integrated to obtain the final alignment between the sequences, resulting in a comprehensive MSA that leverages the efficiency of BWT and the accuracy of wavefront alignment.