Looking for Darwin in Genomic Sequences—Validity and Success of Statistical Methods

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes

(2011) P. Markova-Raina et al.   GENOME RESEARCH

Evolution of adaptive phenotypic traits without positive Darwinian selection

(2011) A L Hughes   HEREDITY

Evolutionary Models Accounting for Layers of Selection in Protein-Coding Genes and their Impact on the Inference of Positive Selection

(2011) N. D. Rubinstein et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

dN/dS-Based Methods Detect Positive Selection Linked to Trade-Offs between Different Fitness Traits in the Coat Protein of Potato virus Y

(2011) B. Moury et al.   MOLECULAR BIOLOGY AND EVOLUTION

Statistical Properties of the Branch-Site Test of Positive Selection

(2010) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict

(2010) C. Deng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment

(2009) Adrian Schneider et al.   Genome Biology and Evolution

Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes

(2008) Austin L. Hughes et al.   IMMUNOGENETICS

Likelihood-Based Clustering (LiBaC) for Codon Models, a Method for Grouping Sites according to Similarities in the Underlying Process of Evolution

(2008) Le Bao et al.   MOLECULAR BIOLOGY AND EVOLUTION

Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models

(2008) M. Anisimova et al.   MOLECULAR BIOLOGY AND EVOLUTION