For a large number of short sequences,
try an experimental service (2017/Jul).
Finished a maintenance, Nov. 9.
Performance has improved but still the new system may be unstable.
If you notice any troubles, let us know (2017/Nov/9).
- Some jobs were canceled around 4:00PM, Nov. 7 (JST) due to overload.
- All jobs were canceled at 8:50AM, Nov. 9 (JST), to migrate this service to the new system.
- Network trouble around 11:20AM, Nov. 9 (JST).
- Network trouble, 3:30AM – 7:30AM, Nov. 10 (JST).
- Network trouble, 4:30AM – 8:30AM, Nov. 17 (JST).
Multiple sequence alignment and NJ / UPGMA phylogeny
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)
(0.0 - 1.0)
- 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