RIMD, Osaka Univ. Osaka Univ.
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

This option is not for SARS-CoV-2.  To align full-length genomes of SARS-CoV-2, try another experimental option (2020/Apr).

This service is experimental, 2017/Aug.  Upper limit of data size and other settings may be changed after trying actual cases.

Multiple alignment of a large number of short and highly similar sequences

Typical data size is up to ∼200,000 sequences × ∼5,000 sites (including gaps), but depends on similarity.  Not for long genomic sequences. 
Upload DNA or protein sequences (FASTA format) in a plain text file (example)
or a .zip file containing a single plain text file (example)

or paste sequences (FASTA format) here: 


UPPERCASE / lowercase:

Direction of nucleotide sequences: Help Updated!

Output order:

Title length in Clustal format (only first word is used as title):

(10 – 100)

Job name (optional):

(basic Latin alphabet, number and space only)

Notify when finished (optional; recommended when submitting large data):

Email address:

Advanced settings

Progressive methods with chained guide trees: Help

Tree-based progressive methods: Help

Partially iterative refinement methods (for less than 100,000 sequences): Help

Memory usage (effective for FFT-NS-1, FFT-NS-2 and mafft-sparsecore): Help


Scoring matrix for amino acid sequences:

Scoring matrix for nucleotide sequences:

↑ Switch it to '1PAM / κ=2' when aligning closely related DNA sequences.

Gap opening penalty: (1.0 – 5.0)

Offset value: (0.0 – 1.0)

Score of N in nucleotide data: example
↓ Long stretches of Ns tend to be gapped (excluded from the alignment).

Experimental option (2016/Apr/26)

↑ Try this if Ns should be aligned with usual letters.

Plot LAST hits (DNA only):





  • Katoh, Rozewicki, Yamada 2019 (Briefings in Bioinformatics 20:1160-1166) Access the recommendation on F1000
    MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

  • Kuraku, Zmasek, Nishimura, Katoh 2013 (Nucleic Acids Research 41:W22-W28)
    aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity