The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
A Fast Algorithm for Joint Reconstruction of Ancestral Amino Acid Sequences
Abstract
A dynamic programming algorithm is developed for maximum-likelihood reconstruction of the set of all ancestral amino acid sequences in a phylogenetic tree. To date, exhaustive algorithms that find the most likely set of ancestral states (joint reconstruction) have running times that scale exponentially with the number of sequences and are thus limited to very few taxa. The time requirement of our new algorithm scales linearly with the number of sequences and is therefore applicable to practically any number of taxa. A detailed description of the new algorithm and an example of its application to cytochrome b sequences are provided.
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Maximum likelihood ancestral trait reconstruction using a continuous time Markov model of evolution was implemented for categorical traits.
“we implemented maximum likelihood ancestral trait reconstruction using a continuous time Markov model of evolution; a framework that has been commonly applied to categorical traits (Pagel 1994; Pupko et al. 2000; Paradis et al. 2004).”
From RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution (2024) · cites this paper as Pupko et al. 2000
Reconstruction certainty depends on inferred phylogeny branch lengths, which are related to evolutionary rates.
“Reconstruction certainty, among many factors, depends on inferred phylogeny branch lengths which are related to evolutionary rates.”
From RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution (2024) · cites this paper as Pupko et al. 2000
Many ancestral likelihood inference methods model the probability of phenotype change as a function of branch length.
“many ancestral likelihood inference methods model the probability of phenotype change as a function of branch length (Pagel 1994; Pupko et al. 2000; Paradis et al. 2004).”
From RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution (2024) · cites this paper as Pupko et al. 2000
Citations
Cites
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
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Research works printed but not linked: 7
- 1971, Syst. Zool., 20, 406, 10.2307/2412116 · DOI
- 1992, Comput. Appl. Biosci., 8, 275
- 1990, J. Mol. Evol., 31, 151, 10.1007/BF02109483 · DOI
- 1996, J. Mol. Evol., 42, 313, 10.1007/BF02198858 · DOI
- 1987, Mol. Biol. Evol., 4, 406
- 1999, Mol. Biol. Evol., 16, 590, 10.1093/oxfordjournals.molbev.a026141 · DOI
- 1998, J. Mol. Evol., 47, 686, 10.1007/PL00006427 · DOI
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PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879
CAFE 5 models variation in evolutionary rates among gene families
Mendes, F. K., Vanderpool, D., Fulton, B., & Hahn, M. W. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btaa1022 · Cited by 833
Evolution of Stress-Regulated Gene Expression in Duplicate Genes of Arabidopsis thaliana
Zou, C., Lehti-Shiu, M. D., Thomashow, M., & Shiu, S.-H. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000581 · Cited by 149
Beale, M. A., Marks, M., Cole, M. J., Lee, M.-K., Pitt, R., Ruis, C., Balla, E., Crucitti, T., Ewens, M., Fernández-Naval, C., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-01000-z · Cited by 135
The origin of mitochondria in light of a fluid prokaryotic chromosome model
Esser, C., Martin, W., & Dagan, T. (2007) · Biology Letters · doi:10.1098/rsbl.2006.0582 · Cited by 92
Redlich, R., Kowalczyk, A., Tene, M., Sestili, H. H., Foley, K., Saputra, E., Clark, N., Chikina, M., Meyer, W. K., & Pfenning, A. R. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae210 · Cited by 14
Metadata
- Authors
- Pupko, T., Pe, I., Shamir, R., & Graur, D.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2000-06-01
- Volume
- 17
- Issue
- 6
- Pages
- 890-896
- ISSN
- 0737-4038
- 1537-1719
- Cited by
- 313
- References
- 1
- Language
- en
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