As an essential step in comparative analyses of biological sequences, multiple sequence alignment (MSA) is still a very challenging problem in bioinformatics, especially in the era of big data. To meet the challenge of big data, MAFFT, a very popular MSA program, has significantly improved in performance and usability recently. In this article, Katoh et al. described in detail the web interface for newly added options for large data, as well as interactive usage to refine sequence data sets and MSAs, which will facilitate users in handling big data and extracting biological information more quickly and effectively by using MAFFT.