Published in BMC Bioinformatics on November 20, 2007
Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Res (2011) 2.41
Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biol (2008) 1.30
Bayesian modeling of recombination events in bacterial populations. BMC Bioinformatics (2008) 1.27
Coalescent simulation of intracodon recombination. Genetics (2009) 1.20
Simulation of molecular data under diverse evolutionary scenarios. PLoS Comput Biol (2012) 1.19
Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets. BMC Evol Biol (2010) 1.17
A survey of genetic simulation software for population and epidemiological studies. Hum Genomics (2008) 1.16
Accurate detection of recombinant breakpoints in whole-genome alignments. PLoS Comput Biol (2009) 1.06
An overview of population genetic data simulation. J Comput Biol (2011) 1.01
Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences. BMC Bioinformatics (2014) 0.99
Population dynamics of Neisseria gonorrhoeae in Shanghai, China: a comparative study. BMC Infect Dis (2010) 0.93
πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios. BMC Bioinformatics (2014) 0.93
Protein evolution along phylogenetic histories under structurally constrained substitution models. Bioinformatics (2013) 0.87
Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories. Mol Biol Evol (2014) 0.87
Nucleotide substitutions in dengue virus serotypes from Asian and American countries: insights into intracodon recombination and purifying selection. BMC Microbiol (2013) 0.86
Characterization of reticulate networks based on the coalescent with recombination. Mol Biol Evol (2008) 0.84
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes. PLoS Comput Biol (2016) 0.84
Mutation rate switch inside Eurasian mitochondrial haplogroups: impact of selection and consequences for dating settlement in Europe. PLoS One (2011) 0.82
Computer programs and methodologies for the simulation of DNA sequence data with recombination. Front Genet (2013) 0.81
Evaluation of methods for detecting conversion events in gene clusters. BMC Bioinformatics (2011) 0.78
SimBac: simulation of whole bacterial genomes with homologous recombination. Microb Genom (2016) 0.78
Spatial and temporal simulation of human evolution. Methods, frameworks and applications. Curr Genomics (2014) 0.76
Trends in substitution models of molecular evolution. Front Genet (2015) 0.75
A Visualization Tool for Calculating the Genetic Substitution Patterns Between Two Different Groups. Evol Bioinform Online (2015) 0.75
How good are indirect tests at detecting recombination in human mtDNA? G3 (Bethesda) (2013) 0.75
The Bacterial Sequential Markov Coalescent. Genetics (2017) 0.75
Evolution in Mendelian Populations. Genetics (1931) 138.42
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol (1986) 36.06
Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics (2002) 34.50
A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol (1994) 19.91
HyPhy: hypothesis testing using phylogenies. Bioinformatics (2004) 17.33
Approximate Bayesian computation in population genetics. Genetics (2002) 13.06
The causes and consequences of HIV evolution. Nat Rev Genet (2004) 4.34
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics (2003) 3.89
SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics (2004) 3.81
Fast "coalescent" simulation. BMC Genet (2006) 2.80
SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography. J Hered (2001) 2.45
msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots. Bioinformatics (2006) 2.45
Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol Biol Evol (2002) 2.36
Bayesian analysis of an admixture model with mutations and arbitrarily linked markers. Genetics (2005) 2.29
The evolutionary genomics of pathogen recombination. Nat Rev Genet (2003) 2.00
CoaSim: a flexible environment for simulating genetic data under coalescent models. BMC Bioinformatics (2005) 1.96
Evolution and ecology of MHC molecules: from genomics to sexual selection. Trends Ecol Evol (1998) 1.83
Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genet Res (2003) 1.79
Using approximate Bayesian computation to estimate tuberculosis transmission parameters from genotype data. Genetics (2006) 1.68
A coalescent model of recombination hotspots. Genetics (2003) 1.60
Comparative evaluation of a new effective population size estimator based on approximate bayesian computation. Genetics (2004) 1.49
Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites. Genetics (2005) 1.41
Simulating haplotype blocks in the human genome. Bioinformatics (2003) 1.31
Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method. Mol Biol Evol (2006) 1.23
Evolution of intrahost HIV-1 genetic diversity during chronic infection. Evolution (2006) 1.11
Using coalescent simulations to test the impact of quaternary climate cycles on divergence in an alpine plant-insect association. Evolution (2006) 1.04
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
ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics (2011) 8.68
Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol (2006) 5.94
ALTER: program-oriented conversion of DNA and protein alignments. Nucleic Acids Res (2010) 5.32
GARD: a genetic algorithm for recombination detection. Bioinformatics (2006) 4.88
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
Tree scanning: a method for using haplotype trees in phenotype/genotype association studies. Genetics (2004) 1.87
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
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
Using models of nucleotide evolution to build phylogenetic trees. Dev Comp Immunol (2005) 1.00
Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy. Infect Genet Evol (2007) 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
Widespread gene conversion of alpha-2-fucosyltransferase genes in mammals. J Mol Evol (2009) 0.87
Phylodynamics of HIV-1 from a phase-III AIDS vaccine trial in North America. Mol Biol 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
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
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
Phylogenetic affinities of Comoroan and East African day geckos (genus Phelsuma): multiple natural colonisations, introductions and island radiations. Mol Phylogenet Evol (2006) 0.81
Proving universal common ancestry with similar sequences. Trends Evol Biol (2012) 0.81
HIV-1 infected monozygotic twins: a tale of two outcomes. BMC Evol Biol (2011) 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
Origin and length distribution of unidirectional prokaryotic overlapping genes. G3 (Bethesda) (2014) 0.77
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