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Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation
&NA; Proteins have distinct structural and functional constraints at different sites that lead to site‐specific preferences for particular amino acid residues as the sequences evolve. HeterogeneityExpand
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A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny
BackgroundWidely used substitution models for proteins, such as the Jones-Taylor-Thornton (JTT) or Whelan and Goldman (WAG) models, are based on empirical amino acid interchange matrices estimatedExpand
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Rapid divergence of codon usage patterns within the rice genome
BackgroundSynonymous codon usage varies widely between genomes, and also between genes within genomes. Although there is now a large body of data on variations in codon usage, it is still not clearExpand
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  • Open Access
On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: data quality and confounding factors.
The correlation between genomic G+C content and optimal growth temperature in prokaryotes has gained renewed interest after Musto et al. [H. Musto, H. Naya, A. Zavala, H. Romero, F. Alvarex-Valin, G.Expand
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Testing for covarion-like evolution in protein sequences.
The covarion hypothesis of molecular evolution proposes that selective pressures on an amino acid or nucleotide site change through time, thus causing changes of evolutionary rate along the edges ofExpand
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  • Open Access
PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis
BackgroundThe covarion hypothesis of molecular evolution holds that selective pressures on a given amino acid or nucleotide site are dependent on the identity of other sites in the molecule thatExpand
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The Relative Importance of Modeling Site Pattern Heterogeneity Versus Partition-Wise Heterotachy in Phylogenomic Inference.
Large taxa-rich genome-scale data sets are often necessary for resolving ancient phylogenetic relationships. But accurate phylogenetic inference requires that they are analyzed with realistic modelsExpand
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Topological Estimation Biases with Covarion Evolution
Covarion processes allow changes in evolutionary rates at sites along the branches of a phylogenetic tree. Covarion-like evolution is increasingly recognized as an important mode of proteinExpand
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An amino acid substitution-selection model adjusts residue fitness to improve phylogenetic estimation.
Standard protein phylogenetic models use fixed rate matrices of amino acid interchange derived from analyses of large databases. Differences between the stationary amino acid frequencies of theseExpand
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  • Open Access
The Site-Wise Log-Likelihood Score is a Good Predictor of Genes under Positive Selection
The strength and direction of selection on the identity of an amino acid residue in a protein is typically measured by the ratio of the rate of non-synonymous substitutions to the rate of synonymousExpand
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