| MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods | 2011/05/04 | English | 31,904 |
| MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 | 2013/10/16 | English | 31,772 |
| MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets | 2016/03/22 | English | 31,428 |
| MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability | 2013/01/16 | English | 25,711 |
| MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms | 2018/05/02 | English | 22,716 |
| MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 | 2007/04/18 | English | 22,622 |
| IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies | 2014/11/03 | English | 13,279 |
| PAML 4: Phylogenetic Analysis by Maximum Likelihood | 2007/04/18 | English | 8,963 |
| Median-joining networks for inferring intraspecific phylogenies | 1999/01/01 | English | 8,491 |
| jModelTest: Phylogenetic Model Averaging | 2008/04/03 | English | 8,158 |
| Bayesian Phylogenetics with BEAUti and the BEAST 1.7 | 2012/02/25 | English | 7,828 |
| Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis | 2000/04/01 | English | 7,445 |
| MEGA11: Molecular Evolutionary Genetics Analysis Version 11 | 2021/04/23 | English | 5,977 |
| Application of Phylogenetic Networks in Evolutionary Studies | 2005/10/12 | English | 5,838 |
| IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era | 2020/02/03 | English | 4,634 |
| UFBoot2: Improving the Ultrafast Bootstrap Approximation | 2017/10/25 | English | 4,527 |
| PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses | 2012/01/20 | English | 4,381 |
| SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building | 2009/10/23 | English | 4,242 |
| The neighbor-joining method: a new method for reconstructing phylogenetic trees. | 1987/07/01 | English | 4,206 |
| DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets | 2017/09/18 | English | 3,655 |
| FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix | 2009/04/17 | English | 3,314 |
| Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference | 1999/08/01 | English | 3,101 |
| Ultrafast Approximation for Phylogenetic Bootstrap | 2013/02/15 | English | 2,486 |
| Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences | 2005/02/09 | English | 2,329 |
| Microsatellite Null Alleles and Estimation of Population Differentiation | 2006/12/05 | English | 2,133 |
| An Improved General Amino Acid Replacement Matrix | 2008/04/03 | English | 2,133 |
| A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach | 2001/05/01 | English | 2,005 |
| Bayesian Inference of Species Trees from Multilocus Data | 2009/11/11 | English | 1,877 |
| BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes | 2021/07/28 | English | 1,752 |
| Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection | 2005/01/12 | English | 1,717 |