L-INS-i is a subtype of the MAFFT alignment which uses local alignment (Smith-Waterman). L-INS-i can align a set of sequences containing sequences flanking around one alignable domain. Flanking sequences are ignored in the pairwise alignment by the Smith-Waterman algorithm. Note that the input sequences are assumed to have only one alignable domain. In benchmark tests, the ref4 of BAliBASE corresponds to this. The other categories of BAliBASE also correspond to similar situations, because they have flanking sequences. L-INS-i also shows higher accuracy values for a part of SABmark and HOMSTRAD than G-INS-i, but we have not identified the reason for this. It has the most accurate alignment settings and is recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information
Parent program: mafft
MAFFT is a multiple sequence alignment program for amino acid or nucleotide sequences that uses fast Fourier transform and simplified scoring system to rapidly identify homologous regions between sequences. MAFFT performs well in reducing CPU time required for multiple sequence alignment and allows an increased the accuracy of alignments even for sequences with large insertions or extensions as well as distantly related sequences of similar length. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of < 200 sequences), FFT-NS-2 (fast; for alignment of < 30,000 sequences), etc. The type of input sequences (amino acid or nucleotide) is automatically recognized.