# | Title | Journal | Year | Citations |
---|
1 | Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 | Genome Biology | 2014 | 58,325 |
2 | The neighbor-joining method: a new method for reconstructing phylogenetic trees. | Molecular Biology and Evolution | 1987 | 49,040 |
3 | MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 | Molecular Biology and Evolution | 2013 | 37,728 |
4 | MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets | Molecular Biology and Evolution | 2016 | 36,708 |
5 | MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods | Molecular Biology and Evolution | 2011 | 36,550 |
6 | CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP | Evolution; International Journal of Organic Evolution | 1985 | 35,356 |
7 | MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability | Molecular Biology and Evolution | 2013 | 32,012 |
8 | MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 | Molecular Biology and Evolution | 2007 | 25,988 |
9 | A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences | Journal of Molecular Evolution | 1980 | 25,715 |
10 | MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms | Molecular Biology and Evolution | 2018 | 25,630 |
11 | MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space | Systematic Biology | 2012 | 20,458 |
12 | Detecting the number of clusters of individuals using the software structure: a simulation study | Molecular Ecology | 2005 | 18,555 |
13 | Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities | Applied and Environmental Microbiology | 2009 | 18,390 |
14 | Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy | Applied and Environmental Microbiology | 2007 | 17,125 |
15 | IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies | Molecular Biology and Evolution | 2015 | 16,610 |
16 | Confidence Limits on Phylogenies: An Approach Using the Bootstrap | Evolution; International Journal of Organic Evolution | 1985 | 16,574 |
17 | A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood | Systematic Biology | 2003 | 15,438 |
18 | New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 | Systematic Biology | 2010 | 15,166 |
19 | Differential expression analysis for sequence count data | Genome Biology | 2010 | 13,707 |
20 | Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows | Molecular Ecology Resources | 2010 | 13,484 |
21 | ANALYZING TABLES OF STATISTICAL TESTS | Evolution; International Journal of Organic Evolution | 1989 | 13,049 |
22 | Evolutionary trees from DNA sequences: A maximum likelihood approach | Journal of Molecular Evolution | 1981 | 12,784 |
23 | genalex 6: genetic analysis in Excel. Population genetic software for teaching and research | Molecular Ecology Notes | 2006 | 12,505 |
24 | Maximum entropy modeling of species geographic distributions | Ecological Modelling | 2006 | 12,411 |
25 | A Method of Computing the Effectiveness of an Insecticide | Journal of Economic Entomology | 1925 | 11,561 |
26 | Resilience and Stability of Ecological Systems | Annual Review of Ecology, Evolution, and Systematics | 1973 | 11,499 |
27 | PAML 4: Phylogenetic Analysis by Maximum Likelihood | Molecular Biology and Evolution | 2007 | 11,130 |
28 | BEAST: Bayesian evolutionary analysis by sampling trees | BMC Evolutionary Biology | 2007 | 11,072 |
29 | Non-parametric multivariate analyses of changes in community structure | Austral Ecology | 1993 | 11,051 |
30 | ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE | Evolution; International Journal of Organic Evolution | 1984 | 10,475 |
31 | STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method | Conservation Genetics Resources | 2012 | 10,115 |
32 | Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA | Applied and Environmental Microbiology | 1993 | 9,925 |
33 | Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB | Applied and Environmental Microbiology | 2006 | 9,859 |
34 | Median-joining networks for inferring intraspecific phylogenies | Molecular Biology and Evolution | 1999 | 9,666 |
35 | Statistical power analysis for the behavioral sciences | Computers, Environment and Urban Systems | 1990 | 9,576 |
36 | jModelTest: Phylogenetic Model Averaging | Molecular Biology and Evolution | 2008 | 9,343 |
37 | micro-checker: software for identifying and correcting genotyping errors in microsatellite data | Molecular Ecology Notes | 2004 | 9,051 |
38 | Bayesian Phylogenetics with BEAUti and the BEAST 1.7 | Molecular Biology and Evolution | 2012 | 9,040 |
39 | Measures of the Amount of Ecologic Association Between Species | Ecology | 1945 | 8,860 |
40 | Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis | Molecular Biology and Evolution | 2000 | 8,843 |
41 | An Ordination of the Upland Forest Communities of Southern Wisconsin | Ecological Monographs | 1957 | 8,777 |
42 | Phylogenies and the Comparative Method | American Naturalist | 1985 | 8,671 |
43 | TCS: a computer program to estimate gene genealogies | Molecular Ecology | 2000 | 8,515 |
44 | Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. | Molecular Biology and Evolution | 1993 | 8,355 |
45 | ITS primers with enhanced specificity for basidiomycetes ‐ application to the identification of mycorrhizae and rusts | Molecular Ecology | 1993 | 8,354 |
46 | A decimal code for the growth stages of cereals | Weed Research | 1974 | 8,263 |
47 | Genetic Distance between Populations | American Naturalist | 1972 | 8,261 |
48 | Red and photographic infrared linear combinations for monitoring vegetation | Remote Sensing of Environment | 1979 | 7,833 |
49 | Dating of the human-ape splitting by a molecular clock of mitochondrial DNA | Journal of Molecular Evolution | 1985 | 7,690 |
50 | The River Continuum Concept | Canadian Journal of Fisheries and Aquatic Sciences | 1980 | 7,671 |
51 | genepop’007: a complete re‐implementation of the genepop software for Windows and Linux | Molecular Ecology Resources | 2008 | 7,546 |
52 | Particle swarm optimization | Swarm Intelligence | 2007 | 7,503 |
53 | A general and simple method for obtaining R2 from generalized linear mixed‐effects models | Methods in Ecology and Evolution | 2013 | 7,490 |
54 | Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms | ISME Journal | 2012 | 7,430 |
55 | Application of Phylogenetic Networks in Evolutionary Studies | Molecular Biology and Evolution | 2006 | 7,402 |
56 | phytools: an R package for phylogenetic comparative biology (and other things) | Methods in Ecology and Evolution | 2012 | 7,280 |
57 | Estimating F-Statistics for the Analysis of Population Structure | Evolution; International Journal of Organic Evolution | 1984 | 7,180 |
58 | DAVID: Database for Annotation, Visualization, and Integrated Discovery | Genome Biology | 2003 | 7,168 |
59 | Pseudoreplication and the Design of Ecological Field Experiments | Ecological Monographs | 1984 | 7,020 |
60 | UniFrac: a New Phylogenetic Method for Comparing Microbial Communities | Applied and Environmental Microbiology | 2005 | 7,007 |
61 | Google Earth Engine: Planetary-scale geospatial analysis for everyone | Remote Sensing of Environment | 2017 | 6,916 |
62 | Arlequin (version 3.0): An integrated software package for population genetics data analysis | Evolutionary Bioinformatics | 2005 | 6,908 |
63 | Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 | Systematic Biology | 2018 | 6,726 |
64 | Novel methods improve prediction of species’ distributions from occurrence data | Ecography | 2006 | 6,691 |
65 | Generalized linear mixed models: a practical guide for ecology and evolution | Trends in Ecology and Evolution | 2009 | 6,634 |
66 | Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics | International Journal of Systematic and Evolutionary Microbiology | 1987 | 6,622 |
67 | Overview of the radiometric and biophysical performance of the MODIS vegetation indices | Remote Sensing of Environment | 2002 | 6,617 |
68 | Behavioral decisions made under the risk of predation: a review and prospectus | Canadian Journal of Zoology | 1990 | 6,597 |
69 | A Rapid Bootstrap Algorithm for the RAxML Web Servers | Systematic Biology | 2008 | 6,439 |
70 | Nanotoxicology: An Emerging Discipline Evolving from Studies of Ultrafine Particles | Environmental Health Perspectives | 2005 | 6,429 |
71 | Ecological and Evolutionary Responses to Recent Climate Change | Annual Review of Ecology, Evolution, and Systematics | 2006 | 6,374 |
72 | AERONET—A Federated Instrument Network and Data Archive for Aerosol Characterization | Remote Sensing of Environment | 1998 | 6,370 |
73 | Analyzing Tables of Statistical Tests | Evolution; International Journal of Organic Evolution | 1989 | 6,311 |
74 | Collinearity: a review of methods to deal with it and a simulation study evaluating their performance | Ecography | 2013 | 6,250 |
75 | MEGA11: Molecular Evolutionary Genetics Analysis Version 11 | Molecular Biology and Evolution | 2021 | 6,189 |
76 | Approved Lists of Bacterial Names | International Journal of Systematic and Evolutionary Microbiology | 1980 | 6,087 |
77 | An ecological risk index for aquatic pollution control.a sedimentological approach | Water Research | 1980 | 6,086 |
78 | Program MARK: survival estimation from populations of marked animals | Bird Study | 1999 | 5,992 |
79 | IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era | Molecular Biology and Evolution | 2020 | 5,960 |
80 | LARGE AREA HYDROLOGIC MODELING AND ASSESSMENT PART I: MODEL DEVELOPMENT | Journal of the American Water Resources Association | 1998 | 5,953 |
81 | Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform | Applied and Environmental Microbiology | 2013 | 5,923 |
82 | Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies | International Journal of Systematic and Evolutionary Microbiology | 2017 | 5,862 |
83 | EFFECTS OF BIODIVERSITY ON ECOSYSTEM FUNCTIONING: A CONSENSUS OF CURRENT KNOWLEDGE | Ecological Monographs | 2005 | 5,856 |
84 | Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology | International Journal of Systematic and Evolutionary Microbiology | 1994 | 5,819 |
85 | UFBoot2: Improving the Ultrafast Bootstrap Approximation | Molecular Biology and Evolution | 2018 | 5,798 |
86 | TOWARD A METABOLIC THEORY OF ECOLOGY | Ecology | 2004 | 5,745 |
87 | A protocol for data exploration to avoid common statistical problems | Methods in Ecology and Evolution | 2010 | 5,735 |
88 | A review of assessing the accuracy of classifications of remotely sensed data | Remote Sensing of Environment | 1991 | 5,676 |
89 | Predictive habitat distribution models in ecology | Ecological Modelling | 2000 | 5,639 |
90 | Parasitology Meets Ecology on Its Own Terms: Margolis et al. Revisited | Journal of Parasitology | 1997 | 5,608 |
91 | A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests | Forest Ecology and Management | 2010 | 5,535 |
92 | The Problem of Pattern and Scale in Ecology: The Robert H. MacArthur Award Lecture | Ecology | 1992 | 5,366 |
93 | Effects of Habitat Fragmentation on Biodiversity | Annual Review of Ecology, Evolution, and Systematics | 2003 | 5,326 |
94 | BEAST 2: A Software Platform for Bayesian Evolutionary Analysis | PLoS Computational Biology | 2014 | 5,301 |
95 | A new method for non-parametric multivariate analysis of variance | Austral Ecology | 2001 | 5,247 |
96 | The Ensembl Variant Effect Predictor | Genome Biology | 2016 | 5,181 |
97 | Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads | PLoS Computational Biology | 2017 | 5,135 |
98 | Resilience: The emergence of a perspective for social–ecological systems analyses | Global Environmental Change | 2006 | 5,115 |
99 | PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses | Molecular Biology and Evolution | 2012 | 5,083 |
100 | Accelerated Profile HMM Searches | PLoS Computational Biology | 2011 | 5,076 |