| MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms |
3684 |
| UFBoot2: Improving the Ultrafast Bootstrap Approximation |
642 |
| BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics |
279 |
| Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes |
94 |
| DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution |
79 |
| SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model |
73 |
| Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree |
69 |
| HIV-TRACE (TRAnsmission Cluster Engine) a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens |
46 |
| Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent |
34 |
| Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication |
32 |
| RADpainter and fineRADstructure Population Inference from RADseq Data |
28 |
| MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons |
26 |
| Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates |
22 |
| The Neutral Theory in Light of Natural Selection |
22 |
| Estimating Improved Partitioning Schemes for Ultraconserved Elements |
21 |
| PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity |
21 |
| Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets |
20 |
| Mode and Rate of Evolution of Haemosporidian Mitochondrial Genomes: Timing the Radiation of Avian Parasites |
20 |
| LFMM 2: Fast and Accurate Inference of Gene-Environment Associations in Genome-Wide Studies |
19 |
| Genetic Architecture and Selection of Chinese Cattle Revealed by Whole Genome Resequencing |
18 |
| An Overlooked Paleotetraploidization in Cucurbitaceae |
18 |
| Toll-Like Receptor Evolution in Birds: Gene Duplication, Pseudogenization, and Diversifying Selection |
18 |
| MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding |
18 |
| Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases |
17 |
| Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm |
16 |
| Bayesian Inference of Species Networks from Multilocus Sequence Data |
16 |
| Evolutionary Origins of Toll-like Receptor Signaling |
16 |
| Phylogeny Estimation by Integration over Isolation with Migration Models |
16 |
| FADS1 and the Timing of Human Adaptation to Agriculture |
16 |
| Phylogenomic Data Yield New and Robust Insights into the Phylogeny and Evolution of Weevils |
16 |
| Accumulation of Mutational Load at the Edges of a Species Range |
16 |
| Phylogenomic Evidence Overturns Current Conceptions o Social Evolution in Wasps (Vespidae) |
16 |
| Divergent Allele Advantage at Human MHC Genes: Signatures of Past and Ongoing Selection |
16 |
| New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life |
15 |
| Non-B-Form DNA Is Enriched at Centromeres |
14 |
| Genome Evolution of the Obligate Endosymbiont Buchnera aphidicola |
14 |
| Exon-Capture-Based Phylogeny and Diversification of the Venomous Gastropods (Neogastropoda, Conoidea) |
14 |
| Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions |
14 |
| Structural Patching Fosters Divergence of Mitochondrial Ribosomes |
14 |
| The Genome Landscape of Tibetan Sheep Reveals Adaptive Introgression from Argali and the History of Early Human Settlements on the Qinghai-Tibetan Plateau |
14 |
| Estimating TimeTrees with MEGA and the TimeTree Resource |
14 |
| Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids |
13 |
| Homeobox Gene Duplication and Divergence in Arachnids |
13 |
| The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference |
13 |
| Mitochondrial Genomics Reveals Shared Phylogeographic Patterns and Demographic History among Three Periodical Cicada Species Groups |
13 |
| Transoceanic Dispersal and Plate Tectonics Shaped Global Cockroach Distributions: Evidence from Mitochondrial Phylogenomics |
13 |
| Codon Usage Bias in Animals: Disentangling the Effects o Natural Selection, Effective Population Size, and GC-Biased Gene Conversion |
13 |
| Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae) |
13 |
| Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut |
12 |
| Genomic Patterns of Local Adaptation under Gene Flow in Arabidopsis lyrata |
12 |
