The Branch-Site Test of Positive Selection Is Surprisingly Robust but Lacks Power under Synonymous Substitution Saturation and Variation in GC

Efficient Selection of Branch-Specific Models of Sequence Evolution

(2012) Julien Y. Dutheil et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2012) Weiwei Zhai et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of Genome Duplications from Age Distributions Revisited

(2012) Kevin Vanneste et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Anolis Lizard Genome: An Amniote Genome without Isochores

(2011) Matthew K. Fujita et al.   Genome Biology and Evolution

Evolution of adaptive phenotypic traits without positive Darwinian selection

(2011) A L Hughes   HEREDITY

The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome

(2011) D. Kostka et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection

(2011) Sergei L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Performance of Positive Selection Inference by Filtering Unreliable Alignment Regions

(2011) Eyal Privman 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

Detecting positive selection within genomes: the problem of biased gene conversion

(2010) A. Ratnakumar et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evidence of Selection upon Genomic GC-Content in Bacteria

(2010) Falk Hildebrand et al.   PLoS Genetics

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

(2009) Laurent Duret et al.   Annual Review of Genomics and Human Genetics

Databases of homologous gene families for comparative genomics

(2009) Simon Penel et al.   BMC BIOINFORMATICS

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

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

The difficulty of avoiding false positives in genome scans for natural selection

(2009) S. Mallick et al.   GENOME RESEARCH

Reliabilities of identifying positive selection by the branch-site and the site-prediction methods

(2009) M. Nozawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

(2008) R. A. Studer et al.   GENOME RESEARCH

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

(2008) Austin L. Hughes et al.   IMMUNOGENETICS

Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models

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

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics