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CherryML: Scalable Maximum Likelihood Estimation of Phylogenetic Models
Open accessPreprint — published as 10.1038/s41592-023-01917-9 · Paper page
Abstract
Phylogenetic models of molecular evolution are central to diverse problems in biology, but maximum likelihood estimation of model parameters is a computationally expensive task, in some cases prohibitively so. To address this challenge, we here introduce CherryML, a broadly applicable method that achieves several orders of magnitude speedup. We demonstrate its utility by applying it to estimate a general 400 × 400 rate matrix for amino acid co-evolution at protein contact sites.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Metadata
- Authors
- Prillo, S., Deng, Y., Boyeau, P., Li, X., Chen, P.-Y., & Song, Y. S.
- Affiliations
- University of California, Berkeley (US)
- Corresponding author
- Song, Yun S.
- Venue
- Nature Methods
- Publisher
- openRxiv
- Published
- 2022-12-22
- Volume
- 20
- Issue
- 8
- Pages
- 1232-1236
- ISSN
- 1548-7091 (ISSN-L)
- PMC
- PMC10644697
- OpenAlex
- W4382541745
- Cited by
- 13
- References
- 1
- Citations by year
- 2026: 4 · 2025: 6 · 2024: 3
- FWCI
- 1.16
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Code Ocean (public-domain)
- Funders
- U.S. Department of Health and Human Services (R35-GM134922)
- National Institutes of Health
- National Institute of General Medical Sciences (R35GM134922)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- maximum likelihood estimation, phylogenetic models, molecular evolution, composite likelihood, cherry, protein coevolution, contact sites, speedup, protein structure
- MeSH terms
- Algorithms, Models, Genetic, Phylogeny, Proteins, Likelihood Functions, Evolution, Molecular
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