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Bayesian inference of phylogeny and its impact on evolutionary biology. Science (2001) 11.15

ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics (2011) 8.68

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol (2003) 4.70

Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst Biol (2010) 4.32

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Testing the hypothesis of common ancestry. J Theor Biol (2002) 2.03

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A formal test of the theory of universal common ancestry. Nature (2010) 1.50

On the origin of cells and viruses: primordial virus world scenario. Ann N Y Acad Sci (2009) 1.29

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Statistics and truth in phylogenomics. Mol Biol Evol (2011) 1.12

Voodoo and circularity errors. Neuroimage (2012) 1.11

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Biologically inspired phylogenetic models strongly outperform the no common mechanism model. Syst Biol (2011) 0.89

On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence. Biol Direct (2011) 0.88

jModelTest: phylogenetic model averaging. Mol Biol Evol (2008) 44.78

jModelTest 2: more models, new heuristics and parallel computing. Nat Methods (2012) 27.83

ProtTest: selection of best-fit models of protein evolution. Bioinformatics (2005) 19.16

RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics (2010) 9.49

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Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol (2006) 5.94

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Pharmacogenetic study of statin therapy and cholesterol reduction. JAMA (2004) 4.47

The causes and consequences of HIV evolution. Nat Rev Genet (2004) 4.34

An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics (2007) 3.76

An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol (2009) 3.11

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Parallel evolution of the genetic code in arthropod mitochondrial genomes. PLoS Biol (2006) 1.85

Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contact. Evolution (2002) 1.62

A coalescent model of recombination hotspots. Genetics (2003) 1.60

Phylogenetic models of molecular evolution: next-generation data, fit, and performance. J Mol Evol (2013) 1.45

A comparison of phylogenetic network methods using computer simulation. PLoS One (2008) 1.40

Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography. BMC Bioinformatics (2007) 1.27

MtArt: a new model of amino acid replacement for Arthropoda. Mol Biol Evol (2006) 1.27

Perkinsoide chabelardi n. gen., a protozoan parasite with an intermediate evolutionary position: possible cause of the decrease of sardine fisheries? Environ Microbiol (2006) 1.26

The evolutionary value of recombination is constrained by genome modularity. PLoS Genet (2005) 1.26

The effect of recombination on the reconstruction of ancestral sequences. Genetics (2010) 1.25

Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method. Mol Biol Evol (2006) 1.23

Coalescent simulation of intracodon recombination. Genetics (2009) 1.20

Analysing recombination in nucleotide sequences. Mol Ecol Resour (2011) 1.18

Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand. PLoS One (2011) 1.11

Evidence for survival of Pleistocene climatic changes in Northern refugia by the land snail Trochoidea geyeri (Soós 1926) (Helicellinae, Stylommatophora). BMC Evol Biol (2003) 1.10

Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy. Infect Genet Evol (2007) 1.00

Using models of nucleotide evolution to build phylogenetic trees. Dev Comp Immunol (2005) 1.00

Phylogenetic evidence for multiple sympatric ecological diversification in a marine snail. Evolution (2007) 0.97

Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands. BMC Evol Biol (2013) 0.96

GenDecoder: genetic code prediction for metazoan mitochondria. Nucleic Acids Res (2006) 0.95

Characterization of phylogenetic networks with NetTest. BMC Bioinformatics (2010) 0.95

Inverted replication of vertebrate mitochondria. Mol Biol Evol (2008) 0.93

Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trial. Retrovirology (2009) 0.93

Identification of 3 phylogenetically related HIV-1 BG intersubtype circulating recombinant forms in Cuba. J Acquir Immune Defic Syndr (2007) 0.92

Identification of a novel HIV-1 complex circulating recombinant form (CRF18_cpx) of Central African origin in Cuba. AIDS (2005) 0.91

jmodeltest.org: selection of nucleotide substitution models on the cloud. Bioinformatics (2014) 0.89

Phylodynamics of HIV-1 from a phase-III AIDS vaccine trial in North America. Mol Biol Evol (2009) 0.87

Widespread gene conversion of alpha-2-fucosyltransferase genes in mammals. J Mol Evol (2009) 0.87

Disease progression and evolution of the HIV-1 env gene in 24 infected infants. Infect Genet Evol (2007) 0.87

Protein evolution along phylogenetic histories under structurally constrained substitution models. Bioinformatics (2013) 0.87

Lack of temporal structure in the short term HIV-1 evolution within asymptomatic naïve patients. Virology (2007) 0.87

Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories. Mol Biol Evol (2014) 0.87

Genome-wide heterogeneity of nucleotide substitution model fit. Genome Biol Evol (2011) 0.86

Computational design of centralized HIV-1 genes. Curr HIV Res (2010) 0.85

Characterization of reticulate networks based on the coalescent with recombination. Mol Biol Evol (2008) 0.84

Individual sequence variability and functional activities of fibrinogen-related proteins (FREPs) in the Mediterranean mussel (Mytilus galloprovincialis) suggest ancient and complex immune recognition models in invertebrates. Dev Comp Immunol (2010) 0.82

Longitudinal population analysis of dual infection with recombination in two strains of HIV type 1 subtype B in an individual from a Phase 3 HIV vaccine efficacy trial. AIDS Res Hum Retroviruses (2006) 0.82

HIV-1 infected monozygotic twins: a tale of two outcomes. BMC Evol Biol (2011) 0.81

Phylogenetic affinities of Comoroan and East African day geckos (genus Phelsuma): multiple natural colonisations, introductions and island radiations. Mol Phylogenet Evol (2006) 0.81

New approach to an old problem: Incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve the Peltigera canina species complex. Mycologia (2010) 0.80

The evolution of the mitochondrial genetic code in arthropods revisited. Mitochondrial DNA (2012) 0.80

On the phylogenetic placement of human T cell leukemia virus type 1 sequences associated with an Andean mummy. Infect Genet Evol (2005) 0.79

Detection and reduction of microaggregates in insulin preparations. Biotechnol Bioeng (2011) 0.78

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Insights into origins of Human T-cell Lymphotropic Virus Type 1 based on new strains from aboriginal people of Canada. Infect Genet Evol (2012) 0.77

Molecular phylogeny and biogeographic history of the European Maja spider crabs (Decapoda, Majidae). Mol Phylogenet Evol (2009) 0.76

Genetic code prediction for metazoan mitochondria with GenDecoder. Methods Mol Biol (2009) 0.76

Grid selection of models of nucleotide substitution. Stud Health Technol Inform (2010) 0.75

Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes. PLoS One (2012) 0.75

Correction: A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis. PLoS One (2016) 0.75

Flow-induced 2D protein crystallization: characterization of the coupled interfacial and bulk flows. Soft Matter (2015) 0.75