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MAFFT 7.273.1

Amino acid or nucleotide sequences in FASTA format.

Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section.

Distance method must be chosen regarding your data

Valid with 6mer distance

1000 for maximum quality

Offset value, which works like gap extension penalty, for group-to-group alignment. For E-INS-i, 0 is recommended to allow large gaps

1.53 default value

Generate reverse complement sequences, as necessary, and align them together with the remaining sequences

Usefull only for amino acids


  • Katoh, K. and Standley, D. M.(2013). MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability . Molecular Biology and Evolution doi