The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Multiple Alignment of DNA Sequences with MAFFT
Abstract
Multiple alignment of DNA sequences is an important step in various molecular biological analyses. As a large amount of sequence data is becoming available through genome and other large-scale sequencing projects, scalability, as well as accuracy, is currently required for a multiple sequence alignment (MSA) program. In this chapter, we outline the algorithms of an MSA program MAFFT and provide practical advice, focusing on several typical situations a biologist sometimes faces. For genome alignment, which is beyond the scope of MAFFT, we introduce two tools: TBA and MAUVE.
Overview
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.
Integrity signals
Registry
Cites
Statistics
Verification
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.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
Tandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374
LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
Brudno, M., Do, C. B., Cooper, G. M., Kim, M. F., Davydov, E., Program, N. C. S., Green, E. D., Sidow, A., & Batzoglou, S. (2003) · Genome Research · doi:10.1101/gr.926603 · Cited by 1,115
Cited by
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
Self-citationA new bioinformatics analysis tools framework at EMBL-EBI
Goujon, M., McWilliam, H., Li, W., Valentin, F., Squizzato, S., Paern, J., & Lopez, R. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq313 · Cited by 1,846
A molecular phylogeny of living primates
Perelman, P., Johnson, W. E., Roos, C., Seuánez, H. N., Horvath, J. E., Moreira, M. A. M., Kessing, B., Pontius, J., Roelke, M., Rumpler, Y., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001342 · Cited by 1,414
“DNA Sequence Analyses Multiple sequence files for each gene segment amplified were aligned by MAFFT version 6 [69,70], imported into Se-Al ver Figure 2.”
MethodPhylotranscriptomic analysis of the origin and early diversification of land plants
Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N., Ayyampalayam, S., Barker, M. S., Burleigh, J. G., Gitzendanner, M. A., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1323926111 · Cited by 1,252
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
Boni, M. F., Lemey, P., Jiang, X., Lam, T. T.-Y., Perry, B. W., Castoe, T. A., Rambaut, A., & Robertson, D. L. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0771-4 · Cited by 1,014
“Sequences were aligned by MAFTT (Katoh et al., 2009), with a final alignment length of 30927, and used in the analyses below.”
Method
Metadata
- Authors
- Katoh, K., Asimenos, G., & Toh, H.
- Venue
- Methods in Molecular Biology
- Publisher
- Humana Press
- Published
- 2009
- Volume
- 537
- Pages
- 39-64
- ISSN
- 1064-3745 (ISSN-L)
- 1940-6029
- OpenAlex
- W118013854
- Cited by
- 1,438
- References
- 4
- FWCI
- 91.74
- Type
- book chapter
- Language
- en
- Open access
- closed
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Multiple Alignment of DNA Sequences with MAFFT. https://app.cochat.ai/papers/10.1007/978-1-59745-251-9_3
- The paper
- Katoh, K., Asimenos, G., & Toh, H. (2009). Multiple Alignment of DNA Sequences with MAFFT. Methods in Molecular Biology. https://doi.org/10.1007/978-1-59745-251-9_3
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
