ArticleMolecular biology and evolution2013
Estimating empirical codon hidden Markov models.
Article in Molecular biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Rate variation and recurrent sequence errors in pandemic-scale phylogenetics.Nature methods · 2026Article
- Highly Recurrent Multinucleotide Mutations in SARS-CoV-2.Molecular biology and evolution · 2025Article
- Detecting Interspecific Positive Selection Using Convolutional Neural Networks.Molecular biology and evolution · 2025Article
- Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses.Molecular biology and evolution · 2023Article
- Next-generation development and application of codon model in evolution.Frontiers in genetics · 2023Review
- Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2.Genome biology and evolution · 2021Article
- Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes.PloS one · 2021Article
- Improved inference of site-specific positive selection under a generalized parametric codon model when there are multinucleotide mutations and multiple nonsynonymous rates.BMC evolutionary biology · 2019Article
- Multinucleotide mutations cause false inferences of lineage-specific positive selection.Nature ecology & evolution · 2018Article
- Non-Markovian effects on protein sequence evolution due to site dependent substitution rates.BMC bioinformatics · 2016Article
- Gene-wide identification of episodic selection.Molecular biology and evolution · 2015Article
- A generalized mechanistic codon model.Molecular biology and evolution · 2014Article
- An experimentally determined evolutionary model dramatically improves phylogenetic fit.Molecular biology and evolution · 2014Article
- Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures.PLoS computational biology · 2014Article
- Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models.Molecular biology and evolution · 2013Article
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4 authors.
Funding
Abstract
Empirical codon models (ECMs) estimated from a large number of globular protein families outperformed mechanistic codon models in their description of the general process of protein evolution. Among other factors, ECMs implicitly model the influence of amino acid properties and multiple nucleotide substitutions (MNS). However, the estimation of ECMs requires large quantities of data, and until recently, only few suitable data sets were available. Here, we take advantage of several new Drosophila species genomes to estimate codon models from genome-wide data. The availability of large numbers of genomes over varying phylogenetic depths in the Drosophila genus allows us to explore various divergence levels. In consequence, we can use these data to determine the appropriate level of divergence for the estimation of ECMs, avoiding overestimation of MNS rates caused by saturation. To account for variation in evolutionary rates along the genome, we develop new empirical codon hidden Markov models (ecHMMs). These models significantly outperform previous ones with respect to maximum likelihood values, suggesting that they provide a better fit to the evolutionary process. Using ECMs and ecHMMs derived from genome-wide data sets, we devise new likelihood ratio tests (LRTs) of positive selection. We found classical LRTs very sensitive to the presence of MNSs, showing high false-positive rates, especially with small phylogenies. The new LRTs are more conservative than the classical ones, having acceptable false-positive rates and reduced power.
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