A maintenance is planned.
This service will be mostly available but may be sometimes unstable in this period.
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.
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