E-INS-i is a subtype of the MAFFT alignment which uses Needleman-Wunsch algorithm for sequence alignment. G-INS-i assumes that entire region can be aligned and tries to align them globally using the Needleman-Wunsch algorithm; that is, a set of sequences of one domain must be extracted by truncating flanking sequences. In benchmark tests, SABmark and HOMSTRAD correspond to this. MAFFT alignment with *--globalpair* option on. suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global 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.