Cited by 17,027Genomics and Phylogenetic StudiesFractal and DNA sequence analysisAlgorithms and Data Compression

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

Open access
Katoh, K.·2002·Nucleic Acids Research

Abstract

A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/nar/gkf436

Cites

42 of 42 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Katoh, K.
Affiliations
Kyoto University (JP)
Corresponding author
Katoh, K.
Venue
Nucleic Acids Research
Published
2002-07-15
Volume
30
Issue
14
Pages
3059-3066
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
OpenAlex
W2127774996
Cited by
17,027
References
42
Citations by year
2026: 1272 · 2025: 1608 · 2024: 1656 · 2023: 1523 · 2022: 1611 · 2021: 1525 · 2020: 1249 · 2019: 918 · 2018: 836 · 2017: 751 · 2016: 649 · 2015: 619 · 2014: 589 · 2013: 549 · 2012: 471
FWCI
12.43
Type
journal article
Language
en
Open access
Locations
  • Nucleic Acids Research (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
Ministry of Education, Culture, Sports, Science and Technology
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
  • Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
Keywords
MAFFT, multiple sequence alignment, fast Fourier transform, homology detection, progressive alignment, iterative refinement, CPU time reduction, indels
MeSH terms
Computer Simulation, DNA-Directed RNA Polymerases, RNA, Ribosomal, Software, Reproducibility of Results, Sequence Alignment, Spectroscopy, Fourier Transform Infrared

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review