The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny
Open accessAbstract
Multiple sequence alignments are widely used to infer evolutionary relationships, enabling inferences of structure, function, and phylogeny. Standard practice is to construct one alignment by some preferred method and use it in further analysis; however, undetected alignment bias can be problematic. I describe Muscle5, a novel algorithm which constructs an ensemble of high-accuracy alignment with diverse biases by perturbing a hidden Markov model and permuting its guide tree. Confidence in an inference is assessed as the fraction of the ensemble which supports it. Applied to phylogenetic tree estimation, I show that ensembles can confidently resolve topologies with low bootstrap according to standard methods, and conversely that some topologies with high bootstraps are incorrect. Applied to the phylogeny of RNA viruses, ensemble analysis shows that recently adopted taxonomic phyla are probably polyphyletic. Ensemble analysis can improve confidence assessment in any inference from an alignment.
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Cites
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
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa015 · Cited by 16,873
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
Sela, I., Ashkenazy, H., Katoh, K., & Pupko, T. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv318 · Cited by 835
Alignment Uncertainty and Genomic Analysis
Wong, K. M., Suchard, M. A., & Huelsenbeck, J. P. (2008) · Science · doi:10.1126/science.1151532 · Cited by 411
Cited by
Multiple protein structure alignment at scale with FoldMason
Gilchrist, C. L. M., Mirdita, M., & Steinegger, M. (2026) · Science · doi:10.1126/science.ads6733 · Cited by 117
Viroid-like colonists of human microbiomes
Zheludev, I. N., Edgar, R. C., Lopez-Galiano, M. J., de la Peña, M., Babaian, A., Bhatt, A. S., & Fire, A. Z. (2024) · Cell · doi:10.1016/j.cell.2024.09.033 · Cited by 73
Self-citationViroid-like colonists of human microbiomes
Zheludev, I. N., Edgar, R. C., Lopez-Galiano, M. J., de la Peña, M., Babaian, A., Bhatt, A. S., & Fire, A. Z. (2024) · doi:10.1101/2024.01.20.576352 · Cited by 73
Self-citationStructural insights into the iron nitrogenase complex
Schmidt, F. V., Schulz, L., Zarzycki, J., Prinz, S., Oehlmann, N. N., Erb, T. J., & Rebelein, J. G. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01124-2 · Cited by 56
Culbertson, E. M., & Levin, T. C. (2023) · PLOS Biology · doi:10.1371/journal.pbio.3002436 · Cited by 43
Metadata
- Authors
- Edgar, R. C.
- Venue
- Nature Communications
- Published
- 2022-11-15
- Volume
- 13
- Issue
- 1
- Pages
- 6968-6968
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W4309191898
- Cited by
- 1,194
- References
- 5
- FWCI
- 57.38
- Type
- journal article
- Language
- en
- Open access
- gold
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