| # | Title | Journal | Year | Citations |
|---|
| 1 | Arlequin (version 3.0): An integrated software package for population genetics data analysis | Evolutionary Bioinformatics | 2005 | 6,908 |
| 2 | Arlequin (version 3.0): an integrated software package for population genetics data analysis | Evolutionary Bioinformatics | 2007 | 3,416 |
| 3 | Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification | Evolutionary Bioinformatics | 2008 | 673 |
| 4 | A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway | Evolutionary Bioinformatics | 2015 | 390 |
| 5 | LASER: A Maximum Likelihood Toolkit for Detecting Temporal Shifts in Diversification Rates from Molecular Phylogenies | Evolutionary Bioinformatics | 2006 | 266 |
| 6 | Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis | Evolutionary Bioinformatics | 2016 | 227 |
| 7 | PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences | Evolutionary Bioinformatics | 2010 | 203 |
| 8 | Phylogenetic Diversity (PD) and Biodiversity Conservation: Some Bioinformatics Challenges | Evolutionary Bioinformatics | 2006 | 189 |
| 9 | Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges | Evolutionary Bioinformatics | 2007 | 165 |
| 10 | AP2/ERF Transcription Factor in Rice: Genome-Wide Canvas and Syntenic Relationships between Monocots and Eudicots | Evolutionary Bioinformatics | 2012 | 162 |
| 11 | Species Delimitation and Global Biosecurity | Evolutionary Bioinformatics | 2012 | 153 |
| 12 | EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes | Evolutionary Bioinformatics | 2013 | 141 |
| 13 | PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics | Evolutionary Bioinformatics | 2013 | 141 |
| 14 | The Austronesian Basic Vocabulary Database: From Bioinformatics to Lexomics | Evolutionary Bioinformatics | 2008 | 140 |
| 15 | LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies | Evolutionary Bioinformatics | 2007 | 114 |
| 16 | TreSpEx–-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information | Evolutionary Bioinformatics | 2014 | 105 |
| 17 | Structurama: Bayesian Inference of Population Structure | Evolutionary Bioinformatics | 2011 | 95 |
| 18 | Twenty-Five New Viruses Associated with the Drosophilidae (Diptera) | Evolutionary Bioinformatics | 2016 | 92 |
| 19 | TreeCmp: Comparison of Trees in Polynomial Time | Evolutionary Bioinformatics | 2012 | 89 |
| 20 | EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics | Evolutionary Bioinformatics | 2010 | 83 |
| 21 | Evolution of the RALF Gene Family in Plants: Gene Duplication and Selection Patterns | Evolutionary Bioinformatics | 2012 | 70 |
| 22 | aTRAM 2.0: An Improved, Flexible Locus Assembler for NGS Data | Evolutionary Bioinformatics | 2018 | 68 |
| 23 | Comparative Evolutionary Histories of the Fungal Chitinase Gene Family Reveal Non-Random Size Expansions and Contractions due to Adaptive Natural Selection | Evolutionary Bioinformatics | 2008 | 67 |
| 24 | Commensal Viruses of Mosquitoes: Host Restriction, Transmission, and Interaction with Arboviral Pathogens | Evolutionary Bioinformatics | 2016 | 66 |
| 25 | SPR Distance Computation for Unrooted Trees | Evolutionary Bioinformatics | 2008 | 64 |
| 26 | Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome ofOncidium Gower Ramsey | Evolutionary Bioinformatics | 2011 | 60 |
| 27 | Comparative Molecular Evolution of Trichoderma Chitinases in Response to Mycoparasitic Interactions | Evolutionary Bioinformatics | 2010 | 56 |
| 28 | Hedging Our Bets: The Expected Contribution of Species to Future Phylogenetic Diversity | Evolutionary Bioinformatics | 2007 | 53 |
| 29 | Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life | Evolutionary Bioinformatics | 2015 | 53 |
| 30 | A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences | Evolutionary Bioinformatics | 2006 | 51 |
| 31 | Human Dispersal Out of Africa: A Lasting Debate | Evolutionary Bioinformatics | 2015 | 51 |
| 32 | An Improved Implementation of Codon Adaptation Index | Evolutionary Bioinformatics | 2007 | 48 |
| 33 | Identification, Nomenclature, and Evolutionary Relationships of Mitogen-Activated Protein Kinase (MAPK) Genes in Soybean | Evolutionary Bioinformatics | 2013 | 48 |
| 34 | Why should we care about molecular coevolution? | Evolutionary Bioinformatics | 2008 | 48 |
| 35 | Why Bacteriophage Encode Exotoxins and other Virulence Factors | Evolutionary Bioinformatics | 2005 | 46 |
| 36 | Relative Codon Adaptation Index, a Sensitive Measure of Codon Usage Bias | Evolutionary Bioinformatics | 2010 | 46 |
| 37 | Efficient Tree Searches with Available Algorithms | Evolutionary Bioinformatics | 2007 | 41 |
| 38 | Cost-Effective Cloud Computing: A Case Study Using the Comparative Genomics Tool, Roundup | Evolutionary Bioinformatics | 2010 | 41 |
| 39 | Phylogenetic Biodiversity Assessment Based on Systematic Nomenclature | Evolutionary Bioinformatics | 2005 | 40 |
| 40 | SBEToolbox: A Matlab Toolbox for Biological Network Analysis | Evolutionary Bioinformatics | 2013 | 40 |
| 41 | Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions | Evolutionary Bioinformatics | 2018 | 40 |
| 42 | Why bacteriophage encode exotoxins and other virulence factors | Evolutionary Bioinformatics | 2007 | 40 |
| 43 | Estimation of Phylogeny Using a General Markov Model | Evolutionary Bioinformatics | 2005 | 39 |
| 44 | A Novel Model for DNA Sequence Similarity Analysis Based on Graph Theory | Evolutionary Bioinformatics | 2011 | 39 |
| 45 | New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release | Evolutionary Bioinformatics | 2020 | 39 |
| 46 | Bioinformatic Characterization of Mosquito Viromes within the Eastern United States and Puerto Rico: Discovery of Novel Viruses | Evolutionary Bioinformatics | 2016 | 38 |
| 47 | An improved implementation of codon adaptation index | Evolutionary Bioinformatics | 2007 | 38 |
| 48 | A Reduction Algorithm for Computing the Hybridization Number of Two Trees | Evolutionary Bioinformatics | 2007 | 37 |
| 49 | Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods | Evolutionary Bioinformatics | 2014 | 37 |
| 50 | TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing | Evolutionary Bioinformatics | 2015 | 37 |
