Parallel Evolution of Metazoan Mitochondrial Proteins

Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time

(2016) Fábio K. Mendes et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nonadaptive Amino Acid Convergence Rates Decrease over Time

(2015) Richard A. Goldstein et al.   MOLECULAR BIOLOGY AND EVOLUTION

Are Convergent and Parallel Amino Acid Substitutions in Protein Evolution More Prevalent Than Neutral Expectations?

(2015) Zhengting Zou et al.   MOLECULAR BIOLOGY AND EVOLUTION

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution

(2014) Dinara R. Usmanova et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fitness conferred by replaced amino acids declines with time

(2012) S. A. Naumenko et al.   Biology Letters

On the Statistical Interpretation of Site-Specific Variables in Phylogeny-Based Substitution Models

(2012) N. Rodrigue   GENETICS

Epistasis as the primary factor in molecular evolution

(2012) Michael S. Breen et al.   NATURE

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference

(2011) Béatrice Roure et al.   BMC EVOLUTIONARY BIOLOGY

Sequence space and the ongoing expansion of the protein universe

(2010) Inna S. Povolotskaya et al.   NATURE

Identifying Changes in Selective Constraints: Host Shifts in Influenza

(2009) Asif U. Tamuri et al.   PLoS Computational Biology

Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series

(2008) Igor B Rogozin et al.   Biology Direct