ArticleGenetics2013
On the statistical interpretation of site-specific variables in phylogeny-based substitution models.
Article in Genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- A Bayesian Mutation-Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes.Molecular biology and evolution · 2021Article
- Site-Specific Amino Acid Distributions Follow a Universal Shape.Journal of molecular evolution · 2020Article
- Hybrid of Restricted and Penalized Maximum Likelihood Method for Efficient Genome-Wide Association Study.Genes · 2020Article
- Efficient inference, potential, and limitations of site-specific substitution models.Virus evolution · 2020Article
- Detecting amino acid preference shifts with codon-level mutation-selection mixture models.BMC evolutionary biology · 2019Article
- Review
- Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence.Virus evolution · 2018Article
- Sequence entropy of folding and the absolute rate of amino acid substitutions.Nature ecology & evolution · 2017Article
- Parallel Evolution of Metazoan Mitochondrial Proteins.Genome biology and evolution · 2017Article
- Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models.Biology direct · 2017Article
- Finding Direction in the Search for Selection.Journal of molecular evolution · 2017Article
- Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model.Molecular biology and evolution · 2017Article
- Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint.Molecular biology and evolution · 2016Article
- Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server.BMC bioinformatics · 2016Article
- Causes of evolutionary rate variation among protein sites.Nature reviews. Genetics · 2016Review
- Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins.Biology letters · 2015Review
- An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs.Molecular biology and evolution · 2014Article
- An experimentally determined evolutionary model dramatically improves phylogenetic fit.Molecular biology and evolution · 2014Article
- A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.Genetics · 2014Article
- Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package.Bioinformatics (Oxford, England) · 2014Article
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1 author.
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Abstract
Phylogeny-based modeling of heterogeneity across the positions of multiple-sequence alignments has generally been approached from two main perspectives. The first treats site specificities as random variables drawn from a statistical law, and the likelihood function takes the form of an integral over this law. The second assigns distinct variables to each position, and, in a maximum-likelihood context, adjusts these variables, along with global parameters, to optimize a joint likelihood function. Here, it is emphasized that while the first approach directly enjoys the statistical guaranties of traditional likelihood theory, the latter does not, and should be approached with particular caution when the site-specific variables are high dimensional. Using a phylogeny-based mutation-selection framework, it is shown that the difference in interpretation of site-specific variables explains the incongruities in recent studies regarding distributions of selection coefficients.
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