Testing adequacy for DNA substitution models

Improved inference of site-specific positive selection under a generalized parametric codon model when there are multinucleotide mutations and multiple nonsynonymous rates

(2019) Katherine A. Dunn et al.   BMC EVOLUTIONARY BIOLOGY

Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations

(2015) David A. Duchêne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales

(2015) Sebastián Duchêne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Can We Identify Genes with Increased Phylogenetic Reliability?

(2015) Vinson P. Doyle et al.   SYSTEMATIC BIOLOGY

Detection of Implausible Phylogenetic Inferences Using Posterior Predictive Assessment of Model Fit

(2014) Jeremy M. Brown   SYSTEMATIC BIOLOGY

Hessian Calculation for Phylogenetic Likelihood based on the Pruning Algorithm and its Applications

(2012) Toby Kenney et al.   Statistical Applications in Genetics and Molecular Biology

Estimation in Discrete Parameter Models

(2012) Christine Choirat et al.   STATISTICAL SCIENCE

Assessment of Substitution Model Adequacy Using Frequentist and Bayesian Methods

(2010) Jennifer Ripplinger et al.   MOLECULAR BIOLOGY AND EVOLUTION

Effects of Substitution Models on Divergence Time Estimates: Simulations and an Empirical Study of Model Uncertainty Using Cornales

(2010) John J. Schenk et al.   SYSTEMATIC BOTANY

Measuring Fit of Sequence Data to Phylogenetic Model: Gain of Power Using Marginal Tests

(2009) Peter J. Waddell et al.   JOURNAL OF MOLECULAR EVOLUTION

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION