ADAPTSITE: detecting natural selection at single amino acid sites.

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics (2004) 4.22

Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res (2004) 3.00

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates. Proc Natl Acad Sci U S A (2008) 2.34

Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci U S A (2009) 1.94

Models of coding sequence evolution. Brief Bioinform (2008) 1.64

A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Proc Natl Acad Sci U S A (2001) 1.56

Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone. Proc Natl Acad Sci U S A (2002) 1.48

New methods for detecting positive selection at single amino acid sites. J Mol Evol (2004) 1.21

Strong positive selection and recombination drive the antigenic variation of the PilE protein of the human pathogen Neisseria meningitidis. Genetics (2004) 1.19

Multilocus sequence typing of Streptococcus uberis provides sensitive and epidemiologically relevant subtype information and reveals positive selection in the virulence gene pauA. J Clin Microbiol (2005) 1.09

WSPMaker: a web tool for calculating selection pressure in proteins and domains using window-sliding. BMC Bioinformatics (2008) 0.93

Genotype-phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate. Bioinformatics (2009) 0.91

Molecular evolution of α-latrotoxin, the exceptionally potent vertebrate neurotoxin in black widow spider venom. Mol Biol Evol (2013) 0.91

Evolutionary replacement of UV vision by violet vision in fish. Proc Natl Acad Sci U S A (2009) 0.88

Synthesis of Experimental Molecular Biology and Evolutionary Biology: An Example from the World of Vision. Bioscience (2012) 0.86

BoLA class I allele diversity and polymorphism in a herd of cattle. Immunogenetics (2007) 0.86

Genetic polymorphism of the swine major histocompatibility complex ( SLA) class I genes, SLA-1, -2 and -3. Immunogenetics (2003) 0.83

Molecular convergence of infrared vision in snakes. Mol Biol Evol (2010) 0.82

Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level. Mol Biol Evol (2009) 0.81

New methods for inferring population dynamics from microbial sequences. Infect Genet Evol (2006) 0.77

Computational and molecular analysis of conserved influenza A virus RNA secondary structures involved in infectious virion production. RNA Biol (2016) 0.77

Exaptation of Bornavirus-Like Nucleoprotein Elements in Afrotherians. PLoS Pathog (2016) 0.75

Complex evolutionary history of the mammalian histone H1.1-H1.5 gene family. Mol Biol Evol (2017) 0.75

Molecular Function Analysis of Rabies Virus RNA Polymerase L Protein by Using an L Gene-Deficient Virus. J Virol (2017) 0.75

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

MEGA2: molecular evolutionary genetics analysis software. Bioinformatics (2001) 38.50

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

The transcriptional landscape of the mammalian genome. Science (2005) 37.63

Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol (1986) 36.06

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature (2002) 28.79

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

Functional annotation of a full-length mouse cDNA collection. Nature (2001) 23.61

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

DNA data bank of Japan (DDBJ) in collaboration with mass sequencing teams. Nucleic Acids Res (2000) 15.69

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

DNA Data Bank of Japan dealing with large-scale data submission. Nucleic Acids Res (1999) 10.26

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

Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res (2000) 7.88

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

DDBJ in the stream of various biological data. Nucleic Acids Res (2004) 6.24

Large-scale search for genes on which positive selection may operate. Mol Biol Evol (1996) 6.14

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

DDBJ with new system and face. Nucleic Acids Res (2007) 5.33

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

Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res (1986) 4.83

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

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

DNA Data Bank of Japan at work on genome sequence data. Nucleic Acids Res (1998) 4.43

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

Complete nucleotide sequence of an infectious clone of human T-cell leukemia virus type II: an open reading frame for the protease gene. Proc Natl Acad Sci U S A (1985) 4.28

Codon usage tabulated from the GenBank Genetic Sequence Data. Nucleic Acids Res (1988) 4.26

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

DNA Data Bank of Japan (DDBJ) in XML. Nucleic Acids Res (2003) 3.87

Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: proposals for standardization. International Committee on Virus Taxonomy. Arch Virol (1998) 3.77

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

DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Res (2002) 3.64

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

A method for detecting positive selection at single amino acid sites. Mol Biol Evol (1999) 3.58

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

Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res (1990) 3.54

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

Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol (1982) 3.43

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

DDBJ in collaboration with mass-sequencing teams on annotation. Nucleic Acids Res (2005) 3.14

Evolutionary motif and its biological and structural significance. J Mol Evol (1997) 3.03

Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res (1991) 3.01

Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res (1992) 2.95

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

Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol Biol Evol (1999) 2.68

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

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

Molecular cloning and expression of a member of the aquaporin family with permeability to glycerol and urea in addition to water expressed at the basolateral membrane of kidney collecting duct cells. Proc Natl Acad Sci U S A (1994) 2.54

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

Sequence of a novel simian immunodeficiency virus from a wild-caught African mandrill. Nature (1989) 2.45

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

Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts. Proc Natl Acad Sci U S A (1997) 2.35

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

Genome plasticity as a paradigm of eubacteria evolution. J Mol Evol (1997) 2.29

Monophyletic origin and unique dispersal patterns of domestic fowls. Proc Natl Acad Sci U S A (1996) 2.27

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

Rates of evolution of the retroviral oncogene of Moloney murine sarcoma virus and of its cellular homologues. Proc Natl Acad Sci U S A (1985) 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

Mitochondrial DNA polymorphism in Japanese. I. Analysis with restriction enzymes of six base pair recognition. Hum Genet (1984) 2.17

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

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

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

Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Res (1997) 2.10

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

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

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