This option is not for SARS-CoV-2.
To align full-length genomes of SARS-CoV-2, try
another experimental option
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
or a .zip file containing a single plain text file
or paste sequences (FASTA format) here:
UPPERCASE / lowercase
Direction of nucleotide sequences: Help Updated!
Notify when finished
(optional; recommended when submitting large data):
Progressive methods with chained guide trees: Help
Tree-based progressive methods: Help
Partially iterative refinement methods (for less than 100,000 sequences): Help
(effective for FFT-NS-1, FFT-NS-2 and mafft-sparsecore): Help
↑ Switch it to '1PAM / κ=2' when aligning closely related DNA sequences.
Score of N in nucleotide data
↓ Long stretches of Ns tend to be gapped (excluded from the alignment).
↑ Try this if Ns should be aligned with usual letters.
Plot LAST hits
- Katoh, Rozewicki, Yamada 2019
(Briefings in Bioinformatics 20:1160-1166)
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