The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
msa: an R package for multiple sequence alignment
Abstract
Summary: Although the R platform and the add-on packages of the Bioconductor project are widely used in bioinformatics, the standard task of multiple sequence alignment has been neglected so far. The msa package, for the first time, provides a unified R interface to the popular multiple sequence alignment algorithms ClustalW, ClustalOmega and MUSCLE. The package requires no additional software and runs on all major platforms. Moreover, the msa package provides an R interface to the powerful package shade which allows for flexible and customizable plotting of multiple sequence alignments. Availability and implementation: msa is available via the Bioconductor project: http://bioconductor.org/packages/release/bioc/html/msa.html. Further information and the R code of the example presented in this paper are available at http://www.bioinf.jku.at/software/msa/. Contact: bodenhofer@bioinf.jku.at or msa@bioinf.jku.at
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
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
Morgenstern, B. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.3.211 · Cited by 678
Cited by
Gupta, R., Somyajit, K., Narita, T., Maskey, E., Stanlie, A., Kremer, M., Typas, D., Lammers, M., Mailand, N., Nussenzweig, A., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.050 · Cited by 469
The Bio3D packages for structural bioinformatics
Grant, B. J., Skjærven, L., & Yao, X. (2021) · Protein Science · doi:10.1002/pro.3923 · Cited by 462
Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma
Smith, C. C., Beckermann, K. E., Bortone, D. S., De Cubas, A. A., Bixby, L. M., Lee, S. J., Panda, A., Ganesan, S., Bhanot, G., Wallen, E. M., et al. (2018) · Journal of Clinical Investigation · doi:10.1172/jci121476 · Cited by 303
D’Amato, A., Di Cesare Mannelli, L., Lucarini, E., Man, A. L., Le Gall, G., Branca, J. J. V., Ghelardini, C., Amedei, A., Bertelli, E., Regoli, M., et al. (2020) · Microbiome · doi:10.1186/s40168-020-00914-w · Cited by 269
Bile salt hydrolase/aminoacyltransferase shapes the microbiome
Guzior, D., Okros, M., Hernandez, C. M., Shivel, M., Armwald, B., Hausinger, R., & Quinn, R. (2022) · doi:10.21203/rs.3.rs-2050406/v1 · Cited by 187
Metadata
- Authors
- Bodenhofer, U., Bonatesta, E., Horejš-Kainrath, C., & Hochreiter, S.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-08-26
- Volume
- 31
- Issue
- 24
- Pages
- 3997-3999
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2112504441
- Cited by
- 735
- References
- 2
- FWCI
- 6.30
- Type
- journal article
- 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: msa: an R package for multiple sequence alignment. https://app.cochat.ai/papers/10.1093/bioinformatics/btv494
- The paper
- Bodenhofer, U., Bonatesta, E., Horejš-Kainrath, C., & Hochreiter, S. (2015). msa: an R package for multiple sequence alignment. Bioinformatics. https://doi.org/10.1093/bioinformatics/btv494
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.
