Cited by 2,849Genomics and Phylogenetic StudiesRNA and protein synthesis mechanismsEvolution and Genetic Dynamics

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A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach

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Whelan, Simon, Goldman, Nick·2001·Molecular Biology and Evolution

DOI 10.1093/oxfordjournals.molbev.a003851

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Abstract

Phylogenetic inference from amino acid sequence data uses mainly empirical models of amino acid replacement and is therefore dependent on those models. Two of the more widely used models, the Dayhoff and JTT models, are estimated using similar methods that can utilize large numbers of sequences from many unrelated protein families but are somewhat unsatisfactory because they rely on assumptions that may lead to systematic error and discard a large amount of the information within the sequences. The alternative method of maximum-likelihood estimation may utilize the information in the sequence data more efficiently and suffers from no systematic error, but it has previously been applicable to relatively few sequences related by a single phylogenetic tree. Here, we combine the best attributes of these two methods using an approximate maximum-likelihood method. We implemented this approach to estimate a new model of amino acid replacement from a database of globular protein sequences comprising 3,905 amino acid sequences split into 182 protein families. While the new model has an overall structure similar to those of other commonly used models, there are significant differences. The new model outperforms the Dayhoff and JTT models with respect to maximum-likelihood values for a large majority of the protein families in our database. This suggests that it provides a better overall fit to the evolutionary process in globular proteins and may lead to more accurate phylogenetic tree estimates. Potentially, this matrix, and the methods used to generate it, may also be useful in other areas of research, such as biological sequence database searching, sequence alignment, and protein structure prediction, for which an accurate description of amino acid replacement is required.

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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Saitou, N., & Nei, M. (1987) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040454 · Cited by 59,959
The rapid generation of mutation data matrices from protein sequences
Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992) · Computer applications in the biosciences · doi:10.1093/bioinformatics/8.3.275 · Cited by 7,003
PAML: a program package for phylogenetic analysis by maximum likelihood
Yang, Z. (1997) · Computer applications in the biosciences · doi:10.1093/bioinformatics/13.5.555 · Cited by 5,377
Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies
Strimmer, K., & von Haeseler, A. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025664 · Cited by 2,531
A new method of inference of ancestral nucleotide and amino acid sequences.
Yang, Z., Kumar, S., & Nei, M. (1995) · Genetics · doi:10.1093/genetics/141.4.1641 · Cited by 703
Model of Amino Acid Substitution in Proteins Encoded by Mitochondrial DNA
Adachi, J., & Hasegawa, M. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02498640 · Cited by 514
Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation.
Yang, Z., Goldman, N., & Friday, A. (1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040112 · Cited by 433
Self-citation
Models of amino acid substitution and applications to mitochondrial protein evolution
Yang, Z., Nielsen, R., & Hasegawa, M. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025888 · Cited by 414
Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution
Goldman, N., Thorne, J. L., & Jones, D. T. (1998) · Genetics · doi:10.1093/genetics/149.1.445 · Cited by 281
Self-citation
Models of Molecular Evolution and Phylogeny: Table 1.Preprint
Liò, P., & Goldman, N. (1998) · Genome Research · doi:10.1101/gr.8.12.1233 · Cited by 281
Self-citation

Show all 18 references

Research works printed but not linked: 4

Dayhoff, M. O., R. V. Eck, and C. M. Park. 1972. A model of evolutionary change in proteins. Pp. 89–99 in M. O. Dayhoff, ed. Atlas of protein sequence and structure. Vol. 5. National Biomedical Research Foundation, Washington, D.C.
Dayhoff, M. O., R. M. Schwartz, and B. C. Orcutt. 1978. A model of evolutionary change in proteins. Pp. 345–352 in M. O. Dayhoff, ed. Atlas of protein sequence and structure. Vol. 5, suppl. 3. National Biomedical Research Foundation, Washington, D.C.
Lindgren, B. W. 1976. Statistical theory. 3rd edition. Macmillan, New York.
Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pp. 407–514 in D. M. Hillis, C. Moritz, and B. K. Mable, eds. Molecular systematics. Sinauer, Sunderland, Mass.

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Authors: Whelan, S., & Goldman, N.
Affiliations: University of Cambridge (GB)
ORCID: Goldman, Nick
Venue: Molecular Biology and Evolution
Publisher: Oxford University Press (OUP)
Published: 2001-05
Volume: 18
Issue: 5
Pages: 691-699
ISSN: 0737-4038 (ISSN-L)
1537-1719
DOI: 10.1093/oxfordjournals.molbev.a003851
OpenAlex: W2062018285
Cited by: 2,849
References: 18
Citations by year: 2026: 66 · 2025: 95 · 2024: 114 · 2023: 113 · 2022: 138 · 2021: 184 · 2020: 153 · 2019: 143 · 2018: 123 · 2017: 131 · 2016: 111 · 2015: 145 · 2014: 175 · 2013: 142 · 2012: 150
FWCI: 11.31
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: Molecular Biology and Evolution (publishedVersion)
PubMed (publishedVersion)
Research Explorer (The University of Manchester) (publishedVersion)
Funders: Wellcome Trust
Biotechnology and Biological Sciences Research Council
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: protein evolution, amino acid substitution models, maximum likelihood estimation, globular proteins, protein families, phylogenetic inference, sequence alignment
MeSH terms: Algorithms, Amino Acid Sequence, Amino Acids, Computer Simulation, Models, Biological, Phylogeny, Probability, Proteins, Likelihood Functions, Sequence Alignment, Evolution, Molecular

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A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach

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