MEGA2: molecular evolutionary genetics analysis software.

Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics (2003) 53.11

MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform (2008) 24.69

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res (2005) 8.38

Inference of bacterial microevolution using multilocus sequence data. Genetics (2006) 7.93

Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, Burkholderia pseudomallei and Burkholderia mallei. J Clin Microbiol (2003) 7.38

rpoB-based identification of nonpigmented and late-pigmenting rapidly growing mycobacteria. J Clin Microbiol (2003) 5.41

Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A (2004) 5.35

Evolutionary models of the emergence of methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother (2003) 5.29

New DNA viruses identified in patients with acute viral infection syndrome. J Virol (2005) 5.26

Microevolution and history of the plague bacillus, Yersinia pestis. Proc Natl Acad Sci U S A (2004) 5.04

Human infection with an avian H9N2 influenza A virus in Hong Kong in 2003. J Clin Microbiol (2005) 5.04

DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar. Philos Trans R Soc Lond B Biol Sci (2005) 4.84

spa typing method for discriminating among Staphylococcus aureus isolates: implications for use of a single marker to detect genetic micro- and macrovariation. J Clin Microbiol (2004) 4.80

An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res (2006) 4.51

Characterization of encapsulated and noncapsulated Haemophilus influenzae and determination of phylogenetic relationships by multilocus sequence typing. J Clin Microbiol (2003) 4.47

Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res (2004) 4.43

Amoebal coculture of "Mycobacterium massiliense" sp. nov. from the sputum of a patient with hemoptoic pneumonia. J Clin Microbiol (2004) 4.32

Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics (2008) 4.25

The interferon-inducible p47 (IRG) GTPases in vertebrates: loss of the cell autonomous resistance mechanism in the human lineage. Genome Biol (2005) 4.21

Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J Mol Evol (2004) 4.08

Candida orthopsilosis and Candida metapsilosis spp. nov. to replace Candida parapsilosis groups II and III. J Clin Microbiol (2005) 3.93

Sequence and structural analysis of BTB domain proteins. Genome Biol (2005) 3.88

A new perspective on Listeria monocytogenes evolution. PLoS Pathog (2008) 3.85

The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis. Proc Natl Acad Sci U S A (2002) 3.82

Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation. Hum Genomics (2005) 3.77

Norovirus and histo-blood group antigens: demonstration of a wide spectrum of strain specificities and classification of two major binding groups among multiple binding patterns. J Virol (2005) 3.74

Full genome-based classification of rotaviruses reveals a common origin between human Wa-Like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains. J Virol (2008) 3.73

Gene sequence-based criteria for identification of new rickettsia isolates and description of Rickettsia heilongjiangensis sp. nov. J Clin Microbiol (2003) 3.59

Sub-grouping of Plasmodium falciparum 3D7 var genes based on sequence analysis of coding and non-coding regions. Malar J (2003) 3.57

The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs. Hum Genomics (2004) 3.53

The multilocus sequence typing network: mlst.net. Nucleic Acids Res (2005) 3.49

Fuzzy species among recombinogenic bacteria. BMC Biol (2005) 3.47

Novel chikungunya virus variant in travelers returning from Indian Ocean islands. Emerg Infect Dis (2006) 3.43

Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proc Natl Acad Sci U S A (2005) 3.37

Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome Res (2004) 3.34

Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis. Plant Physiol (2003) 3.25

Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell (2005) 3.17

Discovery of a novel human picornavirus in a stool sample from a pediatric patient presenting with fever of unknown origin. J Clin Microbiol (2007) 3.16

Characterization of Bacillus cereus isolates associated with fatal pneumonias: strains are closely related to Bacillus anthracis and harbor B. anthracis virulence genes. J Clin Microbiol (2006) 3.15

Silent nucleotide polymorphisms and a phylogeny for Mycobacterium tuberculosis. Emerg Infect Dis (2004) 3.15

Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci U S A (2003) 3.09

Population structure and evolution of the Bacillus cereus group. J Bacteriol (2004) 3.08

Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and Brucella suis. J Bacteriol (2005) 3.05

Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization. PLoS One (2009) 3.03

Molecular analysis of fungal microbiota in samples from healthy human skin and psoriatic lesions. J Clin Microbiol (2006) 3.01

Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution. Genome Res (2003) 2.96

A new approach to estimate parameters of speciation models with application to apes. Genome Res (2007) 2.93

Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J Mol Evol (2004) 2.91

The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis. Plant Physiol (2003) 2.91

Sequence typing and comparison of population biology of Campylobacter coli and Campylobacter jejuni. J Clin Microbiol (2005) 2.88

The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. PLoS Biol (2005) 2.88

Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res (2002) 2.88

Nuclear protein phosphatases with Kelch-repeat domains modulate the response to brassinosteroids in Arabidopsis. Genes Dev (2004) 2.79

New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biol (2003) 2.77

Genotyping, Orientalis-like Yersinia pestis, and plague pandemics. Emerg Infect Dis (2004) 2.76

RXLR effector reservoir in two Phytophthora species is dominated by a single rapidly evolving superfamily with more than 700 members. Proc Natl Acad Sci U S A (2008) 2.65

A genome-wide survey of R gene polymorphisms in Arabidopsis. Plant Cell (2006) 2.64

Frequency and dynamics of recombination within different species of human enteroviruses. J Virol (2006) 2.64

Evolution of moth sex pheromones via ancestral genes. Proc Natl Acad Sci U S A (2002) 2.64

Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc Natl Acad Sci U S A (2002) 2.63

Gain and loss of multiple genes during the evolution of Helicobacter pylori. PLoS Genet (2005) 2.61

A family of mammalian E3 ubiquitin ligases that contain the UBR box motif and recognize N-degrons. Mol Cell Biol (2005) 2.57

Intra- and interspecific comparisons of bacterial diversity and community structure support coevolution of gut microbiota and termite host. Appl Environ Microbiol (2005) 2.57

Porcine noroviruses related to human noroviruses. Emerg Infect Dis (2005) 2.55

Novel origin of the 1918 pandemic influenza virus nucleoprotein gene. J Virol (2004) 2.55

Phenotypic and molecular characterization of Candida nivariensis sp. nov., a possible new opportunistic fungus. J Clin Microbiol (2005) 2.52

Circulation of endemic type 2 vaccine-derived poliovirus in Egypt from 1983 to 1993. J Virol (2003) 2.51

A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol Biol (2004) 2.51

Coxiella burnetii genotyping. Emerg Infect Dis (2005) 2.50

Phylogenetic evidence for the early evolution of microcystin synthesis. Proc Natl Acad Sci U S A (2003) 2.46

Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res (2005) 2.46

Distribution of surface protein variants among hyperinvasive meningococci: implications for vaccine design. Infect Immun (2004) 2.44

Frequent simian foamy virus infection in persons occupationally exposed to nonhuman primates. J Virol (2004) 2.44

Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell (2003) 2.43

Multiple reassortment between pandemic (H1N1) 2009 and endemic influenza viruses in pigs, United States. Emerg Infect Dis (2011) 2.42

Isolation and identification of actinobacteria from surface-sterilized wheat roots. Appl Environ Microbiol (2003) 2.37

Isolation of strains belonging to the cosmopolitan Polynucleobacter necessarius cluster from freshwater habitats located in three climatic zones. Appl Environ Microbiol (2003) 2.35

Clade replacements in dengue virus serotypes 1 and 3 are associated with changing serotype prevalence. J Virol (2005) 2.35

Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event. J Virol (2005) 2.35

The early stages of duplicate gene evolution. Proc Natl Acad Sci U S A (2003) 2.34

Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proc Natl Acad Sci U S A (2004) 2.33

A novel pancoronavirus RT-PCR assay: frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium. BMC Infect Dis (2005) 2.28

Spotted leaf11, a negative regulator of plant cell death and defense, encodes a U-box/armadillo repeat protein endowed with E3 ubiquitin ligase activity. Plant Cell (2004) 2.28

Mineralized tissue and vertebrate evolution: the secretory calcium-binding phosphoprotein gene cluster. Proc Natl Acad Sci U S A (2003) 2.27

Extended multilocus sequence typing system for Campylobacter coli, C. lari, C. upsaliensis, and C. helveticus. J Clin Microbiol (2005) 2.26

Changes in human immunodeficiency virus type 1 fitness and genetic diversity during disease progression. J Virol (2005) 2.25

Multilocus sequence typing scheme for bacteria of the Bacillus cereus group. Appl Environ Microbiol (2004) 2.24

Recombination in the genesis and evolution of hepatitis B virus genotypes. J Virol (2005) 2.24

The origin and evolution of operons: the piecewise building of the proteobacterial histidine operon. J Mol Evol (2005) 2.23

Cardioviruses are genetically diverse and cause common enteric infections in South Asian children. J Virol (2009) 2.23

A highly divergent picornavirus in a marine mammal. J Virol (2007) 2.23

A Plasmodium falciparum homologue of Plasmodium vivax reticulocyte binding protein (PvRBP1) defines a trypsin-resistant erythrocyte invasion pathway. J Exp Med (2001) 2.22

Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations. PLoS Biol (2005) 2.20

BRITTLE CULM1, which encodes a COBRA-like protein, affects the mechanical properties of rice plants. Plant Cell (2003) 2.19

Genetic diversity within human erythroviruses: identification of three genotypes. J Virol (2002) 2.18

Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae. J Bacteriol (2005) 2.15

Low frequency nonnucleoside reverse-transcriptase inhibitor-resistant variants contribute to failure of efavirenz-containing regimens in treatment- experienced patients. J Infect Dis (2010) 2.15

The causes of phylogenetic conflict in a classic Drosophila species group. Proc Biol Sci (2003) 2.14

Evidence of three maternal lineages in Near Eastern sheep supporting multiple domestication events. Proc Biol Sci (2005) 2.14

Evolutionary deterioration of the vomeronasal pheromone transduction pathway in catarrhine primates. Proc Natl Acad Sci U S A (2003) 2.14

The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol (1987) 266.90

Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A (1979) 41.08

Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol (1993) 38.03

MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Comput Appl Biosci (1994) 28.25

Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci U S A (1973) 26.31

Statistical studies on protein polymorphism in natural populations. I. Distribution of single locus heterozygosity. Genetics (1977) 17.08

Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature (1988) 15.05

Phylogenetic test of the molecular clock and linearized trees. Mol Biol Evol (1995) 14.60

Gene differences between Caucasian, Negro, and Japanese populations. Science (1972) 12.11

Sampling variances of heterozygosity and genetic distance. Genetics (1974) 11.91

A new method of inference of ancestral nucleotide and amino acid sequences. Genetics (1995) 10.23

DNA polymorphism detectable by restriction endonucleases. Genetics (1981) 10.13

The theory of genetic distance and evolution of human races. Jinrui Idengaku Zasshi (1978) 8.80

Relationships between gene trees and species trees. Mol Biol Evol (1988) 8.63

Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J Mol Evol (1983) 7.45

Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol Biol Evol (1990) 5.92

F-statistics and analysis of gene diversity in subdivided populations. Ann Hum Genet (1977) 5.89

Estimation of fixation indices and gene diversities. Ann Hum Genet (1983) 5.67

Genetic structure of human populations. II. Differentiation of blood group gene frequencies among isolated populations. Heredity (Edinb) (1966) 5.55

Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci U S A (1998) 5.54

Maximum likelihood estimation of the number of nucleotide substitutions from restriction sites data. Genetics (1983) 5.48

Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol (1984) 5.39

Studies on the enteropathogenic, facultatively halophilic bacterium, Vibrio parahaemolyticus. 3. Enteropathogenicity. Jpn J Med Sci Biol (1968) 5.35

Linkage disequilibrium in subdivided populations. Genetics (1973) 5.22

Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci. Genetics (1990) 5.11

Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics (1996) 4.55

Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc Natl Acad Sci U S A (1989) 4.52

Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies. J Mol Evol (2000) 4.52

Drift variances of heterozygosity and genetic distance in transient states. Genet Res (1975) 4.45

Molecular phylogeny and divergence times of drosophilid species. Mol Biol Evol (1995) 4.33

Pseudogenes as a paradigm of neutral evolution. Nature (1981) 4.33

Genetic distance and electrophoretic identity of proteins between taxa. J Mol Evol (1973) 4.19

Modification of linkage intensity by natural selection. Genetics (1967) 3.99

Non-random association between electromorphs and inversion chromosomes in finite populations. Genet Res (1980) 3.69

Gene genealogy and variance of interpopulational nucleotide differences. Genetics (1985) 3.64

Infinite allele model with varying mutation rate. Proc Natl Acad Sci U S A (1976) 3.56

Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide. J Mol Evol (1982) 3.45

Involvement of RBP-J in biological functions of mouse Notch1 and its derivatives. Development (1997) 3.42

Population dynamics of sex-determining alleles in honey bees and self-incompatibility alleles in plants. Genetics (1979) 3.27

Measurement of coronary sinus blood flow by continuous thermodilution in man. Circulation (1971) 3.14

p38 and extracellular signal-regulated kinases regulate the myogenic program at multiple steps. Mol Cell Biol (2000) 2.96

Probability of identical monomorphism in related species. Genet Res (1975) 2.91

Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol (2000) 2.86

Genetic variability maintained by mutation and overdominant selection in finite populations. Genetics (1981) 2.79

Genic variation within and between the three major races of man, Caucasoids, Negroids, and Mongoloids. Am J Hum Genet (1974) 2.77

The frequency distribution of lethal chromosomes in finite populations. Proc Natl Acad Sci U S A (1968) 2.76

Statistical Studies on Protein Polymorphism in Natural Populations. III. Distribution of Allele Frequencies and the Number of Alleles per Locus. Genetics (1980) 2.76

Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol (1993) 2.74

Delta-induced Notch signaling mediated by RBP-J inhibits MyoD expression and myogenesis. J Biol Chem (1999) 2.65

Enteropathogenic Escherichia coli associated with diarrhea in children and adults. Jpn J Med Sci Biol (1967) 2.62

Letters to the editors: Lewontin-Krakauer test for neutral genes. Genetics (1975) 2.59

Models of evolution of reproductive isolation. Genetics (1983) 2.58

Serological studies on the cholera group of vibrios. Jpn J Med Sci Biol (1970) 2.55

Phylogenetic analysis of polymorphic DNA sequences at the Adh locus in Drosophila melanogaster and its sibling species. J Mol Evol (1985) 2.48

Interior-branch and bootstrap tests of phylogenetic trees. Mol Biol Evol (1995) 2.45

Human origins and analysis of mitochondrial DNA sequences. Science (1992) 2.43

Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules. Mol Biol Evol (1990) 2.41

Testing the neutral mutation hypothesis by distribution of single locus heterozygosity. Nature (1976) 2.37

Accumulation of mutations in sexual and asexual populations. Genet Res (1987) 2.30

Genetic structure of human populations. I. Local differentiation of blood group gene frequencies in Japan. Heredity (Edinb) (1966) 2.26

The number of nucleotides required to determine the branching order of three species, with special reference to the human-chimpanzee-gorilla divergence. J Mol Evol (1986) 2.25

Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods. J Mol Evol (1997) 2.23

Identity of genes by descent within and between populations under mutation and migration pressures. Theor Popul Biol (1972) 2.19

The stress-induced MAP kinase p38 regulates endocytic trafficking via the GDI:Rab5 complex. Mol Cell (2001) 2.19

Positive darwinian selection observed at the variable-region genes of immunoglobulins. Mol Biol Evol (1989) 2.17

Studies on the enteropathogenic, facultatively halophilic bacterium, Vibrio parahaemolyticus. II. Serological characteristics. Jpn J Med Sci Biol (1968) 2.15

Estimation of mutation rate from rare protein variants. Am J Hum Genet (1977) 2.15

Case-control study of endemic diarrheal disease in Thai children. J Infect Dis (1989) 2.14

Statistical Studies on Protein Polymorphism in Natural Populations II. Gene Differentiation between Populations. Genetics (1978) 2.13

Evolution of human races at the gene level. Prog Clin Biol Res (1982) 2.13

Pitx2 determines left-right asymmetry of internal organs in vertebrates. Nature (1998) 2.10

Molecular typing of enterohemorrhagic Escherichia coli O157:H7 isolates in Japan by using pulsed-field gel electrophoresis. J Clin Microbiol (1997) 2.10

Note on genetic drift and estimation of effective population size. Genetics (1984) 2.07

Induction of cell-membrane porosity by ultrasound. Lancet (1999) 2.06

Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. Mol Biol Evol (1988) 2.03

Molecular variant of angiotensinogen gene is associated with coronary atherosclerosis. Circulation (1995) 2.02

The T-box genes Tbx4 and Tbx5 regulate limb outgrowth and identity. Nature (1999) 2.01

Total number of individuals affected by a single deleterious mutation in a finite population. Am J Hum Genet (1972) 1.98

Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes. Mol Biol Evol (1997) 1.97

Linkage modifications and sex difference in recombination. Genetics (1969) 1.96

Stable linkage disequilibrium without epistasis in subdivided populations. Theor Popul Biol (1974) 1.93

Extinction time of deleterious mutant genes in large populations. Theor Popul Biol (1971) 1.87

Polymorphism and evolution of influenza A virus genes. Mol Biol Evol (1986) 1.86

Bacteriological examination of diarrheal stools in Calcutta. Indian J Med Res (1971) 1.85

Gene duplication and nucleotide substitution in evolution. Nature (1969) 1.85

Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol Biol Evol (1996) 1.84

Mean and variance of FST in a finite number of incompletely isolated populations. Theor Popul Biol (1977) 1.79

Divergent evolution and evolution by the birth-and-death process in the immunoglobulin VH gene family. Mol Biol Evol (1994) 1.77

Effective population size when fertility is inherited. Genet Res (1966) 1.76

Outbreaks of enterohaemorrhagic Escherichia coli O157:H7 infection by two different genotype strains in Japan, 1996. Lancet (1996) 1.75

Somatic antigen variation in Vibrio cholerae. Jpn J Med Sci Biol (1971) 1.71

Radical pancreatectomy for ductal cell carcinoma of the head of the pancreas. Cancer (1989) 1.71

Variability and heritability of human fertility. Ann Hum Genet (1970) 1.71

The transient distribution of allele frequencies under mutation pressure. Genet Res (1976) 1.70

Inoculation of human interleukin-17 gene-transfected Meth-A fibrosarcoma cells induces T cell-dependent tumor-specific immunity in mice. Oncology (2001) 1.68

A note on positive identification of paternity by using genetic markers. Hum Hered (1983) 1.66

Functional conservation of mouse Notch receptor family members. FEBS Lett (1996) 1.65

Evolution of Antennapedia-class homeobox genes. Genetics (1996) 1.63

Houseflies: not simple mechanical vectors of enterohemorrhagic Escherichia coli O157:H7. Am J Trop Med Hyg (1999) 1.59