This service was temporarily unavailable around 16:00, Mar/17 (JST).
If your job had any problems around then, please resubmit the job.
To avoid overload,
a light-weight option,
for MSA of full-length SARS-CoV-2 genomes
For a large number of short sequences,
try an experimental service.
Experimental service for aligning raw reads (2019/Aug)
Multiple sequence alignment and NJ / UPGMA phylogeny
Paste protein or DNA sequences in fasta format. Example
or upload a plain text file:
UPPERCASE / lowercase
Direction of nucleotide sequences
(optional; used as output file name and subject of emails):
Notify when finished
(optional; recommended when submitting large data):
Iterative refinement methods
Align unrelated segments, too?
in Alpha Testing
If the input data is expected to be globally conserved but locally contaminated by unrelated segments, try 'Unalignlevel>0' and possibly 'Leave gappy regions'.
This feature is available only when G-INS-1 or G-INS-i is selected in the Strategy section above.
↑ 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.
To display the tree, follow the “Refine dataset” link in the result page.
(Collects homologs by PSI-BLAST and aligns homologs with input sequences; Protein only):
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