Simulation of Genome-Wide Evolution under Heterogeneous Substitution Models and Complex Multispecies Coalescent Histories

Protein evolution along phylogenetic histories under structurally constrained substitution models

(2013) Miguel Arenas et al.   BIOINFORMATICS

Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation

(2013) J S Lopes et al.   HEREDITY

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

(2013) Walid H. Gharib et al.   MOLECULAR BIOLOGY AND EVOLUTION

Purifying Selection and Molecular Adaptation in the Genome of Verminephrobacter, the Heritable Symbiotic Bacteria of Earthworms

(2012) Kasper U. Kjeldsen et al.   Genome Biology and Evolution

The interface of protein structure, protein biophysics, and molecular evolution

(2012) David A. Liberles et al.   PROTEIN SCIENCE

The genome of murine cytomegalovirus is shaped by purifying selection and extensive recombination

(2012) L.M. Smith et al.   VIROLOGY

Simulation of Molecular Data under Diverse Evolutionary Scenarios

(2012) Miguel Arenas   PLoS Computational Biology

Tools for simulating evolution of aligned genomic regions with integrated parameter estimation

(2012) Avinash Varadarajan et al.   GENOME BIOLOGY

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

(2011) Laurent Excoffier et al.   BIOINFORMATICS

Genome-Wide Heterogeneity of Nucleotide Substitution Model Fit

(2011) Leonardo Arbiza et al.   Genome Biology and Evolution

ALF—A Simulation Framework for Genome Evolution

(2011) Daniel A. Dalquen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Approximate Bayesian Computation in Evolution and Ecology

(2010) Mark A. Beaumont   Annual Review of Ecology Evolution and Systematics

Evidence of positive selection at codon sites localized in extracellular domains of mammalian CC motif chemokine receptor proteins

(2010) Kelsey J Metzger et al.   BMC EVOLUTIONARY BIOLOGY

Coalescent Simulation of Intracodon Recombination

(2009) M. Arenas et al.   GENETICS

INDELible: A Flexible Simulator of Biological Sequence Evolution

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

Genome-wide scans for footprints of natural selection

(2009) T. K. Oleksyk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

GENOMEPOP: A program to simulate genomes in populations

(2008) Antonio Carvajal-Rodríguez   BMC BIOINFORMATICS

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION

Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes

(2008) M. T Holder et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES