E-INS-i is a subtype of the MAFFT alignment which uses local alignment with generalized affine gap costs (Altschul). With E-INS-i, unalignable residues are left unaligned at the pairwise alignment stage, because of the use of the generalized affine gap cost. Therefore E-INS-i is applicable to a difficult problem such as RNA polymerase, which has several conserved motifs embedded in long unalignable regions. As E-INS-i has the minimum assumption of the three methods, this is recommended if the nature of sequences to be aligned is not clear. Note that E-INS-i assumes that the arrangement of the conserved motifs is shared by all sequences. It is mostly suitable for sequences containing large unalignable regions and less than 200 sequences.
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.