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.
Progressive methods with chained guide trees: Help
Tree-based progressive methods: Help
Partially iterative refinement methods (for less than 100,000 sequences): Help
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