Table 1.

Options of version 5.3 (upper) and the previous version (lower) of MAFFT

^aAll pairwise alignments are computed by global alignment with an FFT approximation. The FFT approximation is disabled in the progressive alignment stage.

^bAll pairwise alignments are computed with FASTA (25) with the Smith–Waterman optimization.

^cAll pairwise alignments are computed with FASTA (25) without the Smith–Waterman optimization.

^dDistance matrix is calculated based on the number of 6-tuples shared by two sequences (1,10).

^eUPGMA tree with a modified linkage (for detail see Supplementary Material).

^fGuide tree is recalculated based on the first alignment and progressive alignment is re-performed (1,13).

^g‘Importance’ (I) value is considered as described in text.

^hWSP score is optimized through the iterative refinement (14).