| MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space | 2012/02/22 | English | 17,769 |
| A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood | 2003/10/01 | English | 13,126 |
| New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 | 2010/03/29 | English | 12,462 |
| Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 | 2018/04/27 | English | 5,729 |
| A Rapid Bootstrap Algorithm for the RAxML Web Servers | 2008/10/01 | English | 5,465 |
| Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments | 2007/08/01 | English | 3,744 |
| Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests | 2004/10/01 | English | 2,837 |
| An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis | 1993/06/01 | English | 2,750 |
| Species Concepts and Species Delimitation | 2007/12/01 | English | 2,427 |
| Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects | 2006/08/01 | English | 2,048 |
| Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative | 2006/08/01 | English | 1,945 |
| A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data | 2001/11/01 | English | 1,923 |
| Gene Trees in Species Trees | 1997/09/01 | English | 1,828 |
| An Approximately Unbiased Test of Phylogenetic Tree Selection | 2002/05/01 | English | 1,822 |
| Gaps as Characters in Sequence-Based Phylogenetic Analyses | 2000/06/01 | English | 1,805 |
| Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis | 2008/02/01 | English | 1,635 |
| Procedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts | 1992/03/01 | English | 1,505 |
| Bayesian Phylogenetic Analysis of Combined Data | 2004/02/01 | English | 1,346 |
| Dispersal-Vicariance Analysis: A New Approach to the Quantification of Historical Biogeography | 1997/03/01 | English | 1,188 |
| Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices | 2016/04/26 | English | 1,178 |
| Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks | 2012/09/24 | English | 1,117 |
| Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets | 2013/06/14 | English | 1,080 |
| DNA Barcoding and Taxonomy in Diptera: A Tale of High Intraspecific Variability and Low Identification Success | 2006/10/01 | English | 994 |
| Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology | 1971/12/01 | English | 934 |
| Bayesian Estimation of Ancestral Character States on Phylogenies | 2004/10/01 | English | 892 |
| Phylogenetic Analysis of Covariance by Computer Simulation | 1993/09/01 | English | 878 |
| Model Selection in Historical Biogeography Reveals that Founder-Event Speciation Is a Crucial Process in Island Clades | 2014/08/14 | English | 854 |
| Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales | 2012/01/09 | English | 784 |
| Inferring Phylogeny Despite Incomplete Lineage Sorting | 2006/02/01 | English | 768 |
| Estimating a Binary Character's Effect on Speciation and Extinction | 2007/10/01 | English | 758 |