| # | Title | Journal | Year | Citations |
|---|
| 1 | MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods | Molecular Biology and Evolution | 2011 | 36,550 |
| 2 | MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 | Molecular Biology and Evolution | 2007 | 25,988 |
| 3 | Ancestral polyploidy in seed plants and angiosperms | Nature | 2011 | 1,862 |
| 4 | Genetic Distances and Reconstruction of Phylogenetic Trees From Microsatellite DNA | Genetics | 1996 | 1,038 |
| 5 | MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers | Bioinformatics | 1994 | 711 |
| 6 | Phylogenetic test of the molecular clock and linearized trees. | Molecular Biology and Evolution | 1995 | 694 |
| 7 | A new method of inference of ancestral nucleotide and amino acid sequences. | Genetics | 1995 | 613 |
| 8 | Disintegration of the Scrophulariaceae | American Journal of Botany | 2001 | 523 |
| 9 | Molecular phylogeny and divergence times of drosophilid species. | Molecular Biology and Evolution | 1995 | 506 |
| 10 | Theoretical foundation of the minimum-evolution method of phylogenetic inference. | Molecular Biology and Evolution | 1993 | 503 |
| 11 | Parallel evolution of virulence in pathogenic Escherichia coli | Nature | 2000 | 502 |
| 12 | DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene | Nature Genetics | 1998 | 483 |
| 13 | Sequence variation in the human angiotensin converting enzyme | Nature Genetics | 1999 | 452 |
| 14 | Haplotype Structure and Population Genetic Inferences from Nucleotide-Sequence Variation in Human Lipoprotein Lipase | American Journal of Human Genetics | 1998 | 439 |
| 15 | Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Conservation and Turnover | Molecular Biology and Evolution | 2002 | 411 |
| 16 | A genome triplication associated with early diversification of the core eudicots | Genome Biology | 2012 | 389 |
| 17 | Apolipoprotein E Variation at the Sequence Haplotype Level: Implications for the Origin and Maintenance of a Major Human Polymorphism | American Journal of Human Genetics | 2000 | 377 |
| 18 | Virus-specific cytotoxic T-lymphocyte responses select for amino-acid variation in simian immunodeficiency virus Env and Nef | Nature Medicine | 1999 | 364 |
| 19 | Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth | Plant Journal | 2007 | 361 |
| 20 | Origin of the metazoan phyla: Molecular clocks confirm paleontological estimates | Proceedings of the National Academy of Sciences of the United States of America | 1998 | 328 |
| 21 | Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference | Journal of Molecular Evolution | 1992 | 318 |
| 22 | PHYLOGENETIC ANALYSIS IN MOLECULAR EVOLUTIONARY GENETICS | Annual Review of Genetics | 1996 | 297 |
| 23 | Selectionism and Neutralism in Molecular Evolution | Molecular Biology and Evolution | 2005 | 293 |
| 24 | Rates of Conservative and Radical Nonsynonymous Nucleotide Substitutions in Mammalian Nuclear Genes | Journal of Molecular Evolution | 2000 | 274 |
| 25 | Expression Pattern Shifts Following Duplication Indicative of Subfunctionalization and Neofunctionalization in Regulatory Genes of Arabidopsis | Molecular Biology and Evolution | 2006 | 273 |
| 26 | Origins and evolution of the recA/RAD51 gene family: Evidence for ancient gene duplication and endosymbiotic gene transfer | Proceedings of the National Academy of Sciences of the United States of America | 2006 | 268 |
| 27 | Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods | Journal of Molecular Evolution | 1997 | 256 |
| 28 | Detection of convergent and parallel evolution at the amino acid sequence level | Molecular Biology and Evolution | 1997 | 255 |
| 29 | Evolutionary relationships of human populations on a global scale. | Molecular Biology and Evolution | 1993 | 248 |
| 30 | Expression of floral MADS-box genes in basal angiosperms: implications for the evolution of floral regulators | Plant Journal | 2005 | 247 |
| 31 | Identifying the Basal Angiosperm Node in Chloroplast Genome Phylogenies: Sampling One's Way Out of the Felsenstein Zone | Molecular Biology and Evolution | 2005 | 242 |
| 32 | Phylogenetic Analysis of Enteroaggregative and Diffusely Adherent Escherichia coli | Infection and Immunity | 1999 | 241 |
| 33 | Calibration of Avian Molecular Clocks | Molecular Biology and Evolution | 2001 | 235 |
| 34 | Evolutionary genetic relationships of clones of Salmonella serovars that cause human typhoid and other enteric fevers | Infection and Immunity | 1990 | 233 |
| 35 | Origins and Evolution of MicroRNA Genes in Plant Species | Genome Biology and Evolution | 2012 | 231 |
| 36 | Molecular genetic relationships of the salmonellae | Applied and Environmental Microbiology | 1996 | 223 |
| 37 | Salmonella reference collection B (SARB): strains of 37 serovars of subspecies I | Journal of General Microbiology | 1993 | 219 |
| 38 | Natural selection on Plasmodium surface proteins | Molecular and Biochemical Parasitology | 1995 | 187 |
| 39 | Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants | Proceedings of the National Academy of Sciences of the United States of America | 2016 | 183 |
| 40 | Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites | Molecular Biology and Evolution | 1996 | 178 |
| 41 | Comparison of next generation sequencing technologies for transcriptome characterization | BMC Genomics | 2009 | 168 |
| 42 | To B or Not to B a Flower: The Role of DEFICIENS and GLOBOSA Orthologs in the Evolution of the Angiosperms | Journal of Heredity | 2005 | 166 |
| 43 | Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta | BMC Plant Biology | 2007 | 162 |
| 44 | Molecular genetic basis of allelic polymorphism in malate dehydrogenase (mdh) in natural populations of Escherichia coli and Salmonella enterica. | Proceedings of the National Academy of Sciences of the United States of America | 1994 | 159 |
| 45 | Invasion and maintenance of a gene duplication. | Proceedings of the National Academy of Sciences of the United States of America | 1994 | 159 |
| 46 | Tests of applicability of several substitution models for DNA sequence data. | Molecular Biology and Evolution | 1995 | 159 |
| 47 | Y chromosomal fertility factors kl-2 and kl-3 of Drosophila melanogaster encode dynein heavy chain polypeptides | Proceedings of the National Academy of Sciences of the United States of America | 2000 | 159 |
| 48 | Nucleotide polymorphism and evolution in the glyceraldehyde-3-phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli. | Proceedings of the National Academy of Sciences of the United States of America | 1991 | 157 |
| 49 | POPTREEW: Web Version of POPTREE for Constructing Population Trees from Allele Frequency Data and Computing Some Other Quantities | Molecular Biology and Evolution | 2014 | 156 |
| 50 | Ancestry of unisexual salamanders | Nature | 1992 | 144 |
