| Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies | 1996/09/01 | English | 1,705 |
| TimeTree: A Resource for Timelines, Timetrees, and Divergence Times | 2017/04/06 | English | 1,675 |
| Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit | 1999/12/01 | English | 1,605 |
| Statistical Properties of New Neutrality Tests Against Population Growth | 2002/12/01 | English | 1,588 |
| Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection | 2005/02/09 | English | 1,583 |
| Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper | 2017/04/29 | English | 1,566 |
| Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach | 2002/01/01 | English | 1,373 |
| Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks | 2003/08/29 | English | 1,321 |
| PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses | 2016/12/23 | English | 1,297 |
| BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics | 2017/12/06 | English | 1,296 |
| Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level | 2005/08/24 | English | 1,281 |
| SMS: Smart Model Selection in PhyML | 2017/05/11 | English | 1,206 |
| BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data | 1997/07/01 | English | 1,152 |
| Estimating Synonymous and Nonsynonymous Substitution Rates Under Realistic Evolutionary Models | 2000/01/01 | English | 1,151 |
| ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data | 2016/02/26 | English | 1,110 |
| Markov Chasin Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees | 1999/06/01 | English | 1,049 |
| eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale | 2021/10/01 | English | 1,049 |
| A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process | 2004/06/01 | English | 1,023 |
| Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution | 1998/05/01 | English | 1,006 |
| Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. | 1993/05/01 | English | 972 |
| Building Phylogenetic Trees from Molecular Data with MEGA | 2013/03/13 | English | 949 |
| Codon-Substitution Models for Detecting Molecular Adaptation at Individual Sites Along Specific Lineages | 2002/06/01 | English | 944 |
| Molecular Evolutionary Genetics Analysis (MEGA) for macOS | 2020/01/06 | English | 907 |
| FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1. | 2015/06/30 | English | 896 |
| ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models | 2019/08/21 | English | 877 |
| Estimating the rate of evolution of the rate of molecular evolution | 1998/12/01 | English | 854 |
| Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae) | 1996/03/01 | English | 853 |
| Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty | 2012/03/07 | English | 844 |
| DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution | 2013/04/05 | English | 837 |
| FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection | 2013/02/18 | English | 834 |