MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

This service is experimental, 2019/Aug. 

Upper limit of data size and other settings will be changed after trying actual cases.

  • Fixed bug in loading FASTQ file, 2019/Dec/4.
  • Fixed bug in handling data with many ns, 2019/Dec/5.

Multiple alignment of raw reads by LAST and MAFFT

Paste sequences (<? nt. × <? sequences; original strands from the sequencer) in FASTA or FASTQ format.  Example
More examples for specific cases are in the Parameters panel below.

If the input data has both forward and reverse strands, they'll be automatically flipped as necessary.  Don't flip any sequences in the input, in order to appropriately consider different error patterns between forward and reverse strands. 

Or, upload the input sequences as a plain text file (example)
or a .zip file containing a single plain text file (example):

UPPERCASE / lowercase:

Output order:

Job name (optional; used as output file name and subject of emails):

(basic Latin alphabet, number and space only)

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

Email address:

Advanced settings

For partially overlapping data:
o-o------- -oooo----- ---o-ooo-- -------ooo

lamassemble 🦙   The output does not always include all input sequences.

For fully overlapping data:
o-oooo--oo oooo-ooo-- -ooo---ooo ooo-----oo

MAFFT with parameters estimated by LAST-TRAIN:


Examples for lamassemble  for mafft

Use pairwisely aligned sites by LAST (for partially overlapping data):

Error probability of:

Plot LAST hits (DNA only):




Memory usage: