| # | Title | Journal | Year | Citations |
|---|
| 1 | The neighbor-joining method: a new method for reconstructing phylogenetic trees. | Molecular Biology and Evolution | 1987 | 49,040 |
| 2 | MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 | Molecular Biology and Evolution | 2013 | 37,728 |
| 3 | MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets | Molecular Biology and Evolution | 2016 | 36,708 |
| 4 | MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods | Molecular Biology and Evolution | 2011 | 36,550 |
| 5 | MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability | Molecular Biology and Evolution | 2013 | 32,012 |
| 6 | MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 | Molecular Biology and Evolution | 2007 | 25,988 |
| 7 | MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms | Molecular Biology and Evolution | 2018 | 25,630 |
| 8 | IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies | Molecular Biology and Evolution | 2015 | 16,610 |
| 9 | PAML 4: Phylogenetic Analysis by Maximum Likelihood | Molecular Biology and Evolution | 2007 | 11,130 |
| 10 | Median-joining networks for inferring intraspecific phylogenies | Molecular Biology and Evolution | 1999 | 9,666 |
| 11 | jModelTest: Phylogenetic Model Averaging | Molecular Biology and Evolution | 2008 | 9,343 |
| 12 | Bayesian Phylogenetics with BEAUti and the BEAST 1.7 | Molecular Biology and Evolution | 2012 | 9,040 |
| 13 | Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis | Molecular Biology and Evolution | 2000 | 8,843 |
| 14 | Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. | Molecular Biology and Evolution | 1993 | 8,355 |
| 15 | Application of Phylogenetic Networks in Evolutionary Studies | Molecular Biology and Evolution | 2006 | 7,402 |
| 16 | MEGA11: Molecular Evolutionary Genetics Analysis Version 11 | Molecular Biology and Evolution | 2021 | 6,189 |
| 17 | IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era | Molecular Biology and Evolution | 2020 | 5,960 |
| 18 | UFBoot2: Improving the Ultrafast Bootstrap Approximation | Molecular Biology and Evolution | 2018 | 5,798 |
| 19 | PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses | Molecular Biology and Evolution | 2012 | 5,083 |
| 20 | SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building | Molecular Biology and Evolution | 2010 | 5,075 |
| 21 | Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. | Molecular Biology and Evolution | 1986 | 4,402 |
| 22 | FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix | Molecular Biology and Evolution | 2009 | 4,165 |
| 23 | DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets | Molecular Biology and Evolution | 2017 | 4,056 |
| 24 | Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference | Molecular Biology and Evolution | 1999 | 3,859 |
| 25 | Population growth makes waves in the distribution of pairwise genetic differences. | Molecular Biology and Evolution | 1992 | 3,711 |
| 26 | Ultrafast Approximation for Phylogenetic Bootstrap | Molecular Biology and Evolution | 2013 | 3,123 |
| 27 | PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses | Molecular Biology and Evolution | 2017 | 2,854 |
| 28 | Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences | Molecular Biology and Evolution | 2005 | 2,782 |
| 29 | An Improved General Amino Acid Replacement Matrix | Molecular Biology and Evolution | 2008 | 2,748 |
| 30 | A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach | Molecular Biology and Evolution | 2001 | 2,599 |
| 31 | Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies | Molecular Biology and Evolution | 1996 | 2,447 |
| 32 | Microsatellite Null Alleles and Estimation of Population Differentiation | Molecular Biology and Evolution | 2007 | 2,333 |
| 33 | Bayesian Inference of Species Trees from Multilocus Data | Molecular Biology and Evolution | 2010 | 2,246 |
| 34 | Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper | Molecular Biology and Evolution | 2017 | 2,156 |
| 35 | Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection | Molecular Biology and Evolution | 2005 | 2,095 |
| 36 | Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit | Molecular Biology and Evolution | 1999 | 2,053 |
| 37 | TimeTree: A Resource for Timelines, Timetrees, and Divergence Times | Molecular Biology and Evolution | 2017 | 2,017 |
| 38 | BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes | Molecular Biology and Evolution | 2021 | 1,968 |
| 39 | Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection | Molecular Biology and Evolution | 2005 | 1,965 |
| 40 | Slipped-strand mispairing: a major mechanism for DNA sequence evolution. | Molecular Biology and Evolution | 1987 | 1,885 |
| 41 | Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach | Molecular Biology and Evolution | 2002 | 1,854 |
| 42 | BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics | Molecular Biology and Evolution | 2018 | 1,844 |
| 43 | Statistical Properties of New Neutrality Tests Against Population Growth | Molecular Biology and Evolution | 2002 | 1,770 |
| 44 | ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data | Molecular Biology and Evolution | 2016 | 1,692 |
| 45 | A codon-based model of nucleotide substitution for protein-coding DNA sequences. | Molecular Biology and Evolution | 1994 | 1,678 |
| 46 | Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks | Molecular Biology and Evolution | 2003 | 1,675 |
| 47 | Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. | Molecular Biology and Evolution | 1995 | 1,661 |
| 48 | BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data | Molecular Biology and Evolution | 1997 | 1,658 |
| 49 | Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level | Molecular Biology and Evolution | 2005 | 1,650 |
| 50 | SMS: Smart Model Selection in PhyML | Molecular Biology and Evolution | 2017 | 1,572 |
