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Top Articles

#TitleJournalYearCitations
1Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2Genome Biology201458,325
2The neighbor-joining method: a new method for reconstructing phylogenetic trees.Molecular Biology and Evolution198749,040
3MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0Molecular Biology and Evolution201337,728
4MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger DatasetsMolecular Biology and Evolution201636,708
5MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony MethodsMolecular Biology and Evolution201136,550
6CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAPEvolution; International Journal of Organic Evolution198535,356
7MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and UsabilityMolecular Biology and Evolution201332,012
8MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0Molecular Biology and Evolution200725,988
9A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequencesJournal of Molecular Evolution198025,715
10MEGA X: Molecular Evolutionary Genetics Analysis across Computing PlatformsMolecular Biology and Evolution201825,630
11MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model SpaceSystematic Biology201220,458
12Detecting the number of clusters of individuals using the software structure: a simulation studyMolecular Ecology200518,555
13Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial CommunitiesApplied and Environmental Microbiology200918,390
14Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial TaxonomyApplied and Environmental Microbiology200717,125
15IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood PhylogeniesMolecular Biology and Evolution201516,610
16Confidence Limits on Phylogenies: An Approach Using the BootstrapEvolution; International Journal of Organic Evolution198516,574
17A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum LikelihoodSystematic Biology200315,438
18New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0Systematic Biology201015,166
19Differential expression analysis for sequence count dataGenome Biology201013,707
20Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and WindowsMolecular Ecology Resources201013,484
21ANALYZING TABLES OF STATISTICAL TESTSEvolution; International Journal of Organic Evolution198913,049
22Evolutionary trees from DNA sequences: A maximum likelihood approachJournal of Molecular Evolution198112,784
23genalex 6: genetic analysis in Excel. Population genetic software for teaching and researchMolecular Ecology Notes200612,505
24Maximum entropy modeling of species geographic distributionsEcological Modelling200612,411
25A Method of Computing the Effectiveness of an InsecticideJournal of Economic Entomology192511,561
26Resilience and Stability of Ecological SystemsAnnual Review of Ecology, Evolution, and Systematics197311,499
27PAML 4: Phylogenetic Analysis by Maximum LikelihoodMolecular Biology and Evolution200711,130
28BEAST: Bayesian evolutionary analysis by sampling treesBMC Evolutionary Biology200711,072
29Non-parametric multivariate analyses of changes in community structureAustral Ecology199311,051
30ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTUREEvolution; International Journal of Organic Evolution198410,475
31STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno methodConservation Genetics Resources201210,115
32Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNAApplied and Environmental Microbiology19939,925
33Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARBApplied and Environmental Microbiology20069,859
34Median-joining networks for inferring intraspecific phylogeniesMolecular Biology and Evolution19999,666
35Statistical power analysis for the behavioral sciencesComputers, Environment and Urban Systems19909,576
36jModelTest: Phylogenetic Model AveragingMolecular Biology and Evolution20089,343
37micro-checker: software for identifying and correcting genotyping errors in microsatellite dataMolecular Ecology Notes20049,051
38Bayesian Phylogenetics with BEAUti and the BEAST 1.7Molecular Biology and Evolution20129,040
39Measures of the Amount of Ecologic Association Between SpeciesEcology19458,860
40Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic AnalysisMolecular Biology and Evolution20008,843
41An Ordination of the Upland Forest Communities of Southern WisconsinEcological Monographs19578,777
42Phylogenies and the Comparative MethodAmerican Naturalist19858,671
43TCS: a computer program to estimate gene genealogiesMolecular Ecology20008,515
44Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.Molecular Biology and Evolution19938,355
45ITS primers with enhanced specificity for basidiomycetes ‐ application to the identification of mycorrhizae and rustsMolecular Ecology19938,354
46A decimal code for the growth stages of cerealsWeed Research19748,263
47Genetic Distance between PopulationsAmerican Naturalist19728,261
48Red and photographic infrared linear combinations for monitoring vegetationRemote Sensing of Environment19797,833
49Dating of the human-ape splitting by a molecular clock of mitochondrial DNAJournal of Molecular Evolution19857,690
50The River Continuum ConceptCanadian Journal of Fisheries and Aquatic Sciences19807,671
51genepop’007: a complete re‐implementation of the genepop software for Windows and LinuxMolecular Ecology Resources20087,546
52Particle swarm optimizationSwarm Intelligence20077,503
53A general and simple method for obtaining R2 from generalized linear mixed‐effects modelsMethods in Ecology and Evolution20137,490
54Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platformsISME Journal20127,430
55Application of Phylogenetic Networks in Evolutionary StudiesMolecular Biology and Evolution20067,402
56phytools: an R package for phylogenetic comparative biology (and other things)Methods in Ecology and Evolution20127,280
57Estimating F-Statistics for the Analysis of Population StructureEvolution; International Journal of Organic Evolution19847,180
58DAVID: Database for Annotation, Visualization, and Integrated DiscoveryGenome Biology20037,168
59Pseudoreplication and the Design of Ecological Field ExperimentsEcological Monographs19847,020
60UniFrac: a New Phylogenetic Method for Comparing Microbial CommunitiesApplied and Environmental Microbiology20057,007
61Google Earth Engine: Planetary-scale geospatial analysis for everyoneRemote Sensing of Environment20176,916
62Arlequin (version 3.0): An integrated software package for population genetics data analysisEvolutionary Bioinformatics20056,908
63Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7Systematic Biology20186,726
64Novel methods improve prediction of species’ distributions from occurrence dataEcography20066,691
65Generalized linear mixed models: a practical guide for ecology and evolutionTrends in Ecology and Evolution20096,634
66Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial SystematicsInternational Journal of Systematic and Evolutionary Microbiology19876,622
67Overview of the radiometric and biophysical performance of the MODIS vegetation indicesRemote Sensing of Environment20026,617
68Behavioral decisions made under the risk of predation: a review and prospectusCanadian Journal of Zoology19906,597
69A Rapid Bootstrap Algorithm for the RAxML Web ServersSystematic Biology20086,439
70Nanotoxicology: An Emerging Discipline Evolving from Studies of Ultrafine ParticlesEnvironmental Health Perspectives20056,429
71Ecological and Evolutionary Responses to Recent Climate ChangeAnnual Review of Ecology, Evolution, and Systematics20066,374
72AERONET—A Federated Instrument Network and Data Archive for Aerosol CharacterizationRemote Sensing of Environment19986,370
73Analyzing Tables of Statistical TestsEvolution; International Journal of Organic Evolution19896,311
74Collinearity: a review of methods to deal with it and a simulation study evaluating their performanceEcography20136,250
75MEGA11: Molecular Evolutionary Genetics Analysis Version 11Molecular Biology and Evolution20216,189
76Approved Lists of Bacterial NamesInternational Journal of Systematic and Evolutionary Microbiology19806,087
77An ecological risk index for aquatic pollution control.a sedimentological approachWater Research19806,086
78Program MARK: survival estimation from populations of marked animalsBird Study19995,992
79IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic EraMolecular Biology and Evolution20205,960
80LARGE AREA HYDROLOGIC MODELING AND ASSESSMENT PART I: MODEL DEVELOPMENTJournal of the American Water Resources Association19985,953
81Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing PlatformApplied and Environmental Microbiology20135,923
82Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assembliesInternational Journal of Systematic and Evolutionary Microbiology20175,862
83EFFECTS OF BIODIVERSITY ON ECOSYSTEM FUNCTIONING: A CONSENSUS OF CURRENT KNOWLEDGEEcological Monographs20055,856
84Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in BacteriologyInternational Journal of Systematic and Evolutionary Microbiology19945,819
85UFBoot2: Improving the Ultrafast Bootstrap ApproximationMolecular Biology and Evolution20185,798
86TOWARD A METABOLIC THEORY OF ECOLOGYEcology20045,745
87A protocol for data exploration to avoid common statistical problemsMethods in Ecology and Evolution20105,735
88A review of assessing the accuracy of classifications of remotely sensed dataRemote Sensing of Environment19915,676
89Predictive habitat distribution models in ecologyEcological Modelling20005,639
90Parasitology Meets Ecology on Its Own Terms: Margolis et al. RevisitedJournal of Parasitology19975,608
91A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forestsForest Ecology and Management20105,535
92The Problem of Pattern and Scale in Ecology: The Robert H. MacArthur Award LectureEcology19925,366
93Effects of Habitat Fragmentation on BiodiversityAnnual Review of Ecology, Evolution, and Systematics20035,326
94BEAST 2: A Software Platform for Bayesian Evolutionary AnalysisPLoS Computational Biology20145,301
95A new method for non-parametric multivariate analysis of varianceAustral Ecology20015,247
96The Ensembl Variant Effect PredictorGenome Biology20165,181
97Unicycler: Resolving bacterial genome assemblies from short and long sequencing readsPLoS Computational Biology20175,135
98Resilience: The emergence of a perspective for social–ecological systems analysesGlobal Environmental Change20065,115
99PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic AnalysesMolecular Biology and Evolution20125,083
100Accelerated Profile HMM SearchesPLoS Computational Biology20115,076