cbrc
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

For a large number of short sequences, try an experimental service.

Multiple sequence alignment and NJ / UPGMA phylogeny

Input:
Paste protein or DNA sequences in fasta format.  Example

or upload a plain text file:


         



  Help

UPPERCASE / lowercase:


Direction of nucleotide sequences: Help



Output order:


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

Email address:

Advanced settings

Strategy:

Updated


Progressive methods




Iterative refinement methods


Help  Updated (2015/Jun)


Help


Help


Help

Align unrelated segments, too? in Alpha Testing (2014/Mar)
If the input data is expected to be globally conserved but locally contaminated by unrelated segments, try 'Unalignlevel>0' and possibly 'Leave gappy regions'.

Unalignlevel:
fs0.0 fs0.8

↑ Default
This feature is available only when G-INS-1 or G-INS-i is selected in the Strategy section above.


Parameters:

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.

Guide tree:

   


To display the tree, follow the “Refine dataset” link in the result page.

Mafft-homologs (Collects homologs by PSI-BLAST and aligns homologs with input sequences; Protein only): Help



Number of homologs: (5 – 600)


Threshold: E = (1e-1 – 1e-40)

Plot LAST hits (DNA only):

   


       


Threshold:

References

  • Katoh, Rozewicki, Yamada 2017 (Briefings in Bioinformatics, in press) 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