| # | Title | Journal | Year | Citations |
|---|
| 1 | 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 |
| 2 | genepop’007: a complete re‐implementation of the genepop software for Windows and Linux | Molecular Ecology Resources | 2008 | 7,546 |
| 3 | Inferring weak population structure with the assistance of sample group information | Molecular Ecology Resources | 2009 | 2,931 |
| 4 | MorphoJ: an integrated software package for geometric morphometrics | Molecular Ecology Resources | 2011 | 2,884 |
| 5 | Clumpak: a program for identifying clustering modes and packaging population structure inferences across K | Molecular Ecology Resources | 2015 | 2,411 |
| 6 | PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies | Molecular Ecology Resources | 2020 | 1,605 |
| 7 | NeEstimator v2: re‐implementation of software for the estimation of contemporary effective population size (Ne) from genetic data | Molecular Ecology Resources | 2014 | 1,584 |
| 8 | COLONY: a program for parentage and sibship inference from multilocus genotype data | Molecular Ecology Resources | 2010 | 1,394 |
| 9 | ldne: a program for estimating effective population size from data on linkage disequilibrium | Molecular Ecology Resources | 2008 | 1,071 |
| 10 | Assessing population structure: FST and related measures | Molecular Ecology Resources | 2011 | 967 |
| 11 | Field guide to next‐generation DNA sequencers | Molecular Ecology Resources | 2011 | 940 |
| 12 | msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design | Molecular Ecology Resources | 2008 | 853 |
| 13 | MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics | Molecular Ecology Resources | 2020 | 785 |
| 14 | pophelper: an R package and web app to analyse and visualize population structure | Molecular Ecology Resources | 2017 | 777 |
| 15 | MalAvi: a public database of malaria parasites and related haemosporidians in avian hosts based on mitochondrial cytochrome b lineages | Molecular Ecology Resources | 2009 | 767 |
| 16 | obitools: a unix‐inspired software package for DNA metabarcoding | Molecular Ecology Resources | 2016 | 765 |
| 17 | coancestry: a program for simulating, estimating and analysing relatedness and inbreeding coefficients | Molecular Ecology Resources | 2011 | 758 |
| 18 | Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all‐taxa biotic surveys | Molecular Ecology Resources | 2013 | 696 |
| 19 | Current trends in microsatellite genotyping | Molecular Ecology Resources | 2011 | 676 |
| 20 | The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem | Molecular Ecology Resources | 2016 | 672 |
| 21 | vcfr: a package to manipulate and visualize variant call format data in R | Molecular Ecology Resources | 2017 | 671 |
| 22 | pcadapt: an R package to perform genome scans for selection based on principal component analysis | Molecular Ecology Resources | 2017 | 647 |
| 23 | Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data | Molecular Ecology Resources | 2011 | 608 |
| 24 | ASAP: assemble species by automatic partitioning | Molecular Ecology Resources | 2021 | 575 |
| 25 | Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data | Molecular Ecology Resources | 2010 | 553 |
| 26 | StAMPP: an R package for calculation of genetic differentiation and structure of mixed‐ploidy level populations | Molecular Ecology Resources | 2013 | 541 |
| 27 | smogd: software for the measurement of genetic diversity | Molecular Ecology Resources | 2010 | 536 |
| 28 | Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data | Molecular Ecology Resources | 2015 | 517 |
| 29 | DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer | Molecular Ecology Resources | 2011 | 504 |
| 30 | dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing | Molecular Ecology Resources | 2018 | 473 |
| 31 | seqphase: a web tool for interconverting phase input/output files and fasta sequence alignments | Molecular Ecology Resources | 2010 | 467 |
| 32 | Comparison of FST outlier tests for SNP loci under selection | Molecular Ecology Resources | 2011 | 448 |
| 33 | DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet | Molecular Ecology Resources | 2014 | 431 |
| 34 | Tag jumps illuminated – reducing sequence‐to‐sample misidentifications in metabarcoding studies | Molecular Ecology Resources | 2015 | 429 |
| 35 | metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data | Molecular Ecology Resources | 2015 | 426 |
| 36 | Taxon‐specific PCR for DNA barcoding arthropod prey in bat faeces | Molecular Ecology Resources | 2011 | 421 |
| 37 | StructureSelector: A web‐based software to select and visualize the optimal number of clusters using multiple methods | Molecular Ecology Resources | 2018 | 419 |
| 38 | polysat: an R package for polyploid microsatellite analysis | Molecular Ecology Resources | 2011 | 410 |
| 39 | Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding | Molecular Ecology Resources | 2012 | 404 |
| 40 | The seven deadly sins of DNA barcoding | Molecular Ecology Resources | 2013 | 398 |
| 41 | Skyline‐plot methods for estimating demographic history from nucleotide sequences | Molecular Ecology Resources | 2011 | 393 |
| 42 | Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges | Molecular Ecology Resources | 2011 | 391 |
| 43 | Distance, flow and PCR inhibition: eDNA dynamics in two headwater streams | Molecular Ecology Resources | 2015 | 391 |
| 44 | A practical guide to methods of parentage analysis | Molecular Ecology Resources | 2010 | 386 |
| 45 | Progress towards DNA barcoding of fungi | Molecular Ecology Resources | 2009 | 383 |
| 46 | Genotyping‐in‐Thousands by sequencing (GT‐seq): A cost effective SNP genotyping method based on custom amplicon sequencing | Molecular Ecology Resources | 2015 | 381 |
| 47 | A first look at the Oxford Nanopore MinION sequencer | Molecular Ecology Resources | 2014 | 362 |
| 48 | New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach | Molecular Ecology Resources | 2009 | 358 |
| 49 | Factors influencing detection of eDNA from a stream‐dwelling amphibian | Molecular Ecology Resources | 2014 | 358 |
| 50 | Dsuite ‐ Fast D‐statistics and related admixture evidence from VCF files | Molecular Ecology Resources | 2021 | 356 |
