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. 2019 Jul 19;20(4):1160-1166.
doi: 10.1093/bib/bbx108.

MAFFT Online Service: Multiple Sequence Alignment, Interactive Sequence Choice and Visualization

Free PMC article

MAFFT Online Service: Multiple Sequence Alignment, Interactive Sequence Choice and Visualization

Kazutaka Katoh et al. Brief Bioinform. .
Free PMC article


This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large numbers of sequences is increasing. To extract biologically relevant information from such data, sophistication of algorithms is necessary but not sufficient. Intuitive and interactive tools for experimental biologists to semiautomatically handle large data are becoming important. We are working on development of MAFFT toward these two directions. Here, we explain (i) the Web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and MSAs.

Keywords: multiple sequence alignment; phylogenetic tree; sequence analysis.


Figure 1
Figure 1
Screenshot of input page for large MSAs in MAFFT online service. (AG) are explained in the main text.
Figure 2
Figure 2
Variants of --add option.
Figure 3
Figure 3
Interactive sequence selection. A group of sequences in guide tree (A) is selected at a time in sequence selection window (B). Several options for tree estimation can be selected (C). MSA can be visually checked using MSAViewer (D).

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