Inference of Functional Divergence Among Proteins When the Evolutionary Process is Non-stationary

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

A phylogenetic mixture model for the identification of functionally divergent protein residues

(2011) Daniel Gaston et al.   BIOINFORMATICS

Recombination Detection Under Evolutionary Scenarios Relevant to Functional Divergence

(2011) Rachael A. Bay et al.   JOURNAL OF MOLECULAR EVOLUTION

Statistical Properties of the Branch-Site Test of Positive Selection

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

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

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