For a large number of short sequences,
try an experimental service.
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
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 from SwissProt by BLAST and performs profile-based alignments; Protein only):
Plot LAST hits
- Katoh, Rozewicki, Yamada 2017
(Briefings in Bioinformatics, in press)
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