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ngsTools: methods for population genetics analyses from next-generation sequencing data
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Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1038/nature11532openalex-snapshot
A map of rice genome variation reveals the origin of cultivated rice
inferredcites →https://doi.org/10.1101/gr.157388.113openalex-snapshot
Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation
inferredcites →https://doi.org/10.1371/journal.pone.0037558openalex-snapshot
SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data
inferredcites →https://doi.org/10.1534/genetics.113.154740openalex-snapshot
Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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inferred← citeshttps://doi.org/10.1038/ncomms11693openalex-snapshot
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inferred← citeshttps://doi.org/10.1038/s43247-025-03021-6openalex-snapshot
Mummified cave cheetahs inform rewilding actions in Saudi Arabia
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Rapid vertebrate speciation via isolation, bottlenecks, and drift
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Machine learning improves SNP microarray performance in challenged samples
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glactools: a command-line toolset for the management of genotype likelihoods and allele counts
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Selective Landscapes in newt Immune Genes Inferred from Patterns of Nucleotide Variation
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Fast and accurate estimation of multidimensional site frequency spectra from low-coverage high-throughput sequencing data
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Pervasive Genomic Signatures of Local Adaptation to Altitude Across Highland Specialist Andean Hummingbird Populations
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Reduction of genetic diversity in ‘Alalā (Hawaiian crow; Corvus hawaiiensis ) between the late 1800s and the late 1900s
inferred← citeshttps://doi.org/10.1093/jhered/esw044openalex-snapshot
Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals
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Genetic basis and adaptive implications of temperature-dependent and temperature-independent effects of drought on chickpea reproductive phenology
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Noncoding Variation and Transcriptional Plasticity Promote Thermal Adaptation in Oysters by Altering Energy Metabolism
inferred← citeshttps://doi.org/10.1093/molbev/msac200openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/molbev/msae046openalex-snapshot
Genetic Basis and Evolution of Structural Color Polymorphism in an Australian Songbird
inferred← citeshttps://doi.org/10.1093/molbev/msaf094openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/molbev/msw051openalex-snapshot
Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens
inferred← citeshttps://doi.org/10.1093/molbev/msw283openalex-snapshot
Archaic adaptive introgression in TBX15/WARS2
inferred← citeshttps://doi.org/10.1093/molbev/msx087openalex-snapshot
Pollutants and Insecticides Drive Local Adaptation in African Malaria Mosquitoes
inferred← citeshttps://doi.org/10.1093/molbev/msx226openalex-snapshot
Exome Sequencing Provides Evidence of Polygenic Adaptation to a Fat-Rich Animal Diet in Indigenous Siberian Populations
inferred← citeshttps://doi.org/10.1093/molbev/msy030openalex-snapshot
Signatures of Selection on Standing Genetic Variation Underlie Athletic and Navigational Performance in Racing Pigeons
inferred← citeshttps://doi.org/10.1093/molbev/msy037openalex-snapshot
Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World’s Rarest Hyena Species, the Brown Hyena
inferred← citeshttps://doi.org/10.1093/molbev/msy108openalex-snapshot
Population Genomic Analysis Reveals Contrasting Demographic Changes of Two Closely Related Dolphin Species in the Last Glacial
inferred← citeshttps://doi.org/10.1093/molbev/msy211openalex-snapshot
Genomic Evidence of Local Adaptation to Climate and Diet in Indigenous Siberians
inferred← citeshttps://doi.org/10.1093/molbev/msz259openalex-snapshot
Divergent Selection and Primary Gene Flow Shape Incipient Speciation of a Riparian Tree on Hawaii Island
inferred← citeshttps://doi.org/10.1093/sysbio/syaa053openalex-snapshot
Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent.
inferred← citeshttps://doi.org/10.1093/sysbio/syad026openalex-snapshot
Hybridization and Transgressive Evolution Generate Diversity in an Adaptive Radiation ofAnolisLizards
inferred← citeshttps://doi.org/10.1093/sysbio/syae037openalex-snapshot
Persistent Gene Flow Suggests an Absence of Reproductive Isolation in an African Antelope Speciation Model
inferred← citeshttps://doi.org/10.1098/rspb.2019.1697openalex-snapshot
The genetics of morphological and behavioural island traits in deer mice
inferred← citeshttps://doi.org/10.1098/rspb.2021.0678openalex-snapshot
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inferred← citeshttps://doi.org/10.1098/rstb.2020.0107openalex-snapshot
Sex-biased gene expression and recent sex chromosome turnover
inferred← citeshttps://doi.org/10.1101/009837openalex-snapshot
Reticulate speciation and adaptive introgression in the Anopheles gambiae species complex
inferred← citeshttps://doi.org/10.1101/029561openalex-snapshot
Variation in linked selection and recombination drive genomic divergence during allopatric speciation of European and American aspens
inferred← citeshttps://doi.org/10.1101/068205openalex-snapshot
Chromosome arm specific patterns of polymorphism associated with chromosomal inversions in the major African malaria vector, Anopheles funestus
inferred← citeshttps://doi.org/10.1101/114579openalex-snapshot
The interplay of demography and selection during maize domestication and expansion
inferred← citeshttps://doi.org/10.1101/127688openalex-snapshot
Multiple origin but single domestication led to Oryza sativa
inferred← citeshttps://doi.org/10.1101/2020.02.14.949081openalex-snapshot
Conservation Genomic Analyses of African and Asiatic Cheetahs ( Acinonyx jubatus) Across Their Current and Historical Species Range
inferred← citeshttps://doi.org/10.1101/2020.06.29.178392openalex-snapshot
Limited evidence for parallel evolution among desert adapted Peromyscus deer mice
inferred← citeshttps://doi.org/10.1101/2020.09.08.287292openalex-snapshot
Barriers to gene flow play an important role in miantaining reproductive isolation between two closely related Populus (Salicaceae) species
inferred← citeshttps://doi.org/10.1101/2021.01.30.428904openalex-snapshot
Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium
inferred← citeshttps://doi.org/10.1101/2021.05.19.442026openalex-snapshot
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inferred← citeshttps://doi.org/10.1101/2021.08.05.455235openalex-snapshot
Differential use of multiple genetic sex determination systems in divergent ecomorphs of an African crater lake cichlid
inferred← citeshttps://doi.org/10.1101/2021.11.04.467261openalex-snapshot
Rapid ecological and evolutionary divergence during a poleward range expansion
inferred← citeshttps://doi.org/10.1101/2021.11.08.467072openalex-snapshot
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inferred← citeshttps://doi.org/10.1101/2022.01.26.477940openalex-snapshot
Genetic basis and adaptive implications of temperature-dependent and temperature-independent effects of drought on chickpea phenology
inferred← citeshttps://doi.org/10.1101/2023.04.20.537757openalex-snapshot
Genetic basis of aposematic coloration in a mimetic radiation of poison frogs
inferred← citeshttps://doi.org/10.1101/2023.08.24.554725openalex-snapshot
A deep learning phenotyping method for genetic analysis of 3D micro-CT data
inferred← citeshttps://doi.org/10.1101/2024.03.30.587279openalex-snapshot
Large-effect loci in a duplicated genomic region modulate reproductive phenology in salmon
inferred← citeshttps://doi.org/10.1101/2024.10.10.617593openalex-snapshot
Divergence in the Pelagic Zone: Genomic Signatures of Speciation and Adaptation in the Ctenophore Mnemiopsis
inferred← citeshttps://doi.org/10.1101/2025.08.05.668748openalex-snapshot
Evidence of positive polygenic selection following a series of environmental and demographic disasters in Pacific herring
inferred← citeshttps://doi.org/10.1101/2025.11.26.688640openalex-snapshot
COATswga: A Coverage Optimizing and Accurate Toolkit for fast primer design in selective whole genome amplification
inferred← citeshttps://doi.org/10.1101/302463openalex-snapshot
Inferring Population Structure and Admixture Proportions in Low Depth NGS Data
inferred← citeshttps://doi.org/10.1101/590604openalex-snapshot
Landscape drivers of genomic diversity and divergence in woodland Eucalyptus
inferred← citeshttps://doi.org/10.1101/742361openalex-snapshot
Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent
inferred← citeshttps://doi.org/10.1101/gr.196485.115openalex-snapshot
Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
inferred← citeshttps://doi.org/10.1101/gr.204800.116openalex-snapshot
Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice
inferred← citeshttps://doi.org/10.1111/1440-1703.12545openalex-snapshot
Demographic history of the Malayan tapirs ( Tapirus indicus ) in Southeast Asia
inferred← citeshttps://doi.org/10.1111/1755-0998.12578openalex-snapshot
angsd ‐wrapper: utilities for analysing next‐generation sequencing data
inferred← citeshttps://doi.org/10.1111/1755-0998.12593openalex-snapshot
Practical low‐coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species
inferred← citeshttps://doi.org/10.1111/1755-0998.12758openalex-snapshot
Exploring Approximate Bayesian Computation for inferring recent demographic history with genomic markers in nonmodel species
inferred← citeshttps://doi.org/10.1111/1755-0998.12980openalex-snapshot
A versatile Rapture (RAD‐Capture) platform for genotyping marine turtles
inferred← citeshttps://doi.org/10.1111/1755-0998.13070openalex-snapshot
An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity
inferred← citeshttps://doi.org/10.1111/1755-0998.13153openalex-snapshot
Estimating and accounting for genotyping errors in RAD‐seq experiments
inferred← citeshttps://doi.org/10.1111/1755-0998.13324openalex-snapshot
A reference‐free approach to analyse RADseq data using standard next generation sequencing toolkits
inferred← citeshttps://doi.org/10.1111/2041-210x.14286openalex-snapshot
Population assignment from genotype likelihoods for low‐coverage whole‐genome sequencing data
inferred← citeshttps://doi.org/10.1111/bij.12511openalex-snapshot
Improving the estimation of genetic distances from Next-Generation Sequencing data
inferred← citeshttps://doi.org/10.1111/ddi.13439openalex-snapshot
History, demography and genetic status of Balkan and Caucasian Lynx lynx (Linnaeus, 1758) populations revealed by genome‐wide variation
inferred← citeshttps://doi.org/10.1111/eva.12659openalex-snapshot
Recent advances in conservation and population genomics data analysis
inferred← citeshttps://doi.org/10.1111/eva.13046openalex-snapshot
Genetic architecture, demographic history, and genomic differentiation of Populus davidiana revealed by whole‐genome resequencing
inferred← citeshttps://doi.org/10.1111/eva.13419openalex-snapshot
The influence of genetic architecture on responses to selection under drought in rice
inferred← citeshttps://doi.org/10.1111/eva.13656openalex-snapshot
Genomic evidence for domestication selection in three hatchery populations of Chinook salmon, Oncorhynchus tshawytscha
inferred← citeshttps://doi.org/10.1111/eva.13704openalex-snapshot
Unlocking the secret life of blue mussels: Exploring connectivity in the Skagerrak through biophysical modeling and population genomics
inferred← citeshttps://doi.org/10.1111/eva.70039openalex-snapshot
Prioritizing Conservation Areas for the Hyacinth Macaw ( Anodorhynchus hyacinthinus ) in Brazil From Low‐Coverage Genomic Data
inferred← citeshttps://doi.org/10.1111/eva.70072openalex-snapshot
Genomic Insights Into Red Squirrels in Scotland Reveal Loss of Heterozygosity Associated With Extreme Founder Effects
inferred← citeshttps://doi.org/10.1111/eva.70096openalex-snapshot
Fine Scale Patterns of Population Structure and Connectivity in Scandinavian Flat Oysters in Scandinavia ( Ostrea edulis L.)
inferred← citeshttps://doi.org/10.1111/evo.13110openalex-snapshot
Partitioning the effects of isolation by distance, environment, and physical barriers on genomic divergence between parapatric threespine stickleback
inferred← citeshttps://doi.org/10.1111/jeb.13401openalex-snapshot
Parallel plumage colour evolution and introgressive hybridization in wheatears
inferred← citeshttps://doi.org/10.1111/jse.12911openalex-snapshot
Genomic analyses reveal natural selection on reproduction related genes between two closely related Populus (Salicaceae) species
inferred← citeshttps://doi.org/10.1111/mec.13391openalex-snapshot
Amphibian molecular ecology and how it has informed conservation
inferred← citeshttps://doi.org/10.1111/mec.13596openalex-snapshot
Divergence in gene expression within and between two closely related flycatcher species
inferred← citeshttps://doi.org/10.1111/mec.13732openalex-snapshot
Phylogenetics support an ancient common origin of two scientific icons: Devils Hole and Devils Hole pupfish
inferred← citeshttps://doi.org/10.1111/mec.14264openalex-snapshot
Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations
inferred← citeshttps://doi.org/10.1111/mec.14335openalex-snapshot
Chromosome arm‐specific patterns of polymorphism associated with chromosomal inversions in the major African malaria vector, Anopheles funestus
inferred← citeshttps://doi.org/10.1111/mec.14342openalex-snapshot
Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle ( Dendroctonus ponderosae )
inferred← citeshttps://doi.org/10.1111/mec.14556openalex-snapshot
Rapid divergence of mussel populations despite incomplete barriers to dispersal
inferred← citeshttps://doi.org/10.1111/mec.14853openalex-snapshot
Large‐effect loci affect survival in Tasmanian devils ( Sarcophilus harrisii ) infected with a transmissible cancer
inferred← citeshttps://doi.org/10.1111/mec.14909openalex-snapshot
Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process
inferred← citeshttps://doi.org/10.1111/mec.15115openalex-snapshot
Phenotypic sexual dimorphism is associated with genomic signatures of resolved sexual conflict
inferred← citeshttps://doi.org/10.1111/mec.15176openalex-snapshot
31° South: The physiology of adaptation to arid conditions in a passerine bird
inferred← citeshttps://doi.org/10.1111/mec.15224openalex-snapshot
Host hybridization as a potential mechanism of lateral symbiont transfer in deep‐sea vesicomyid clams
inferred← citeshttps://doi.org/10.1111/mec.15287openalex-snapshot
Landscape drivers of genomic diversity and divergence in woodland Eucalyptus
inferred← citeshttps://doi.org/10.1111/mec.15301openalex-snapshot
Genome‐wide epigenetic isolation by environment in a widespread Anolis lizard
inferred← citeshttps://doi.org/10.1111/mec.15366openalex-snapshot
Genomic patterns in the widespread Eurasian lynx shaped by Late Quaternary climatic fluctuations and anthropogenic impacts
inferred← citeshttps://doi.org/10.1111/mec.15388openalex-snapshot
Evidence for widespread selection in shaping the genomic landscape during speciation of Populus
inferred← citeshttps://doi.org/10.1111/mec.15401openalex-snapshot
Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent
inferred← citeshttps://doi.org/10.1111/mec.15695openalex-snapshot
Historical isolation facilitates species radiation by sexual selection: Insights fromChorthippusgrasshoppers
inferred← citeshttps://doi.org/10.1111/mec.15784openalex-snapshot
Pleistocene climate fluctuations drove demographic history of African golden wolves (Canis lupaster)
inferred← citeshttps://doi.org/10.1111/mec.16077openalex-snapshot
A beginner's guide to low‐coverage whole genome sequencing for population genomics
inferred← citeshttps://doi.org/10.1111/mec.16301openalex-snapshot
A holobiont view of island biogeography: Unravelling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates
inferred← citeshttps://doi.org/10.1111/mec.16406openalex-snapshot
Extensive introgression at late stages of species formation: Insights from grasshopper hybrid zones
inferred← citeshttps://doi.org/10.1111/mec.16577openalex-snapshot
Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus)
inferred← citeshttps://doi.org/10.1111/mec.16604openalex-snapshot
Whole‐genome phylogeography of the blue‐faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo‐Z chromosome
inferred← citeshttps://doi.org/10.1111/mec.16724openalex-snapshot
The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid
inferred← citeshttps://doi.org/10.1111/mec.16928openalex-snapshot
Widespread gene flow following range expansion in Anna's Hummingbird
inferred← citeshttps://doi.org/10.1111/mec.17195openalex-snapshot
Concurrent invasions of European starlings in Australia and North America reveal population‐specific differentiation in shared genomic regions
inferred← citeshttps://doi.org/10.1111/mec.17546openalex-snapshot
Decrypting Corals: Does Regulatory Evolution Underlie Environmental Specialisation of Coral Cryptic Lineages?
inferred← citeshttps://doi.org/10.1111/mec.17547openalex-snapshot
Population Genomics of Adaptive Radiations: Exceptionally High Levels of Genetic Diversity and Recombination in an Endemic Spider From the Canary Islands
inferred← citeshttps://doi.org/10.1111/mec.17600openalex-snapshot
Divergence in Regulatory Regions and Gene Duplications May Underlie Chronobiological Adaptation in Desert Tortoises
inferred← citeshttps://doi.org/10.1111/mec.v28.21openalex-snapshot
Host hybridization as a potential mechanism of lateral symbiont transfer in deep‐sea vesicomyid clams
inferred← citeshttps://doi.org/10.1126/sciadv.1603198openalex-snapshot
The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation
inferred← citeshttps://doi.org/10.1126/sciadv.abi8584openalex-snapshot
Pervasive hybridization with local wild relatives in Western European grapevine varieties
inferred← citeshttps://doi.org/10.1126/sciadv.adu6611openalex-snapshot
Biocultural vulnerability of traditional crops in the Indian Trans-Himalaya
inferred← citeshttps://doi.org/10.1126/science.aam5298openalex-snapshot
Ancient genomic changes associated with domestication of the horse
inferred← citeshttps://doi.org/10.1126/science.aao3297openalex-snapshot
Ancient genomes revisit the ancestry of domestic and Przewalski’s horses
inferred← citeshttps://doi.org/10.1126/science.adw8265openalex-snapshot
The genetics, evolution, and maintenance of a biological rock-paper-scissors game
inferred← citeshttps://doi.org/10.1139/as-2021-0030openalex-snapshot
Low levels of hybridization between sympatric cold-water-adapted Arctic cod and Polar cod in the Beaufort Sea confirm genetic distinctiveness
inferred← citeshttps://doi.org/10.1142/s0219720019500379openalex-snapshot
AUSPP: A universal short-read pre-processing package
inferred← citeshttps://doi.org/10.1177/1176934318775106openalex-snapshot
Detecting the Population Structure and Scanning for Signatures of Selection in Horses ( Equus caballus ) From Whole-Genome Sequencing Data
inferred← citeshttps://doi.org/10.1177/1176934319892284openalex-snapshot
Applications of Next-Generation Sequencing Technologies and Computational Tools in Molecular Evolution and Aquatic Animals Conservation Studies: A Short Review
inferred← citeshttps://doi.org/10.1186/s12859-014-0356-4openalex-snapshot
ANGSD: Analysis of Next Generation Sequencing Data
inferred← citeshttps://doi.org/10.1186/s12859-021-04265-7openalex-snapshot
A novel nonlinear dimension reduction approach to infer population structure for low-coverage sequencing data
inferred← citeshttps://doi.org/10.1186/s12862-018-1209-yopenalex-snapshot
Co-occurrence of ecologically similar species of Hawaiian spiders reveals critical early phase of adaptive radiation
inferred← citeshttps://doi.org/10.1186/s12864-017-3871-7openalex-snapshot
Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum
inferred← citeshttps://doi.org/10.1186/s12864-017-3883-3openalex-snapshot
The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics
inferred← citeshttps://doi.org/10.1186/s12864-018-4721-yopenalex-snapshot
Complex signatures of genomic variation of two non-model marine species in a homogeneous environment
inferred← citeshttps://doi.org/10.1186/s12864-022-08483-yopenalex-snapshot
Transcriptomic analyses of the HPG axis-related tissues reveals potential candidate genes and regulatory pathways associated with egg production in ducks
inferred← citeshttps://doi.org/10.1186/s12915-017-0351-0openalex-snapshot
Population genomics reveals that an anthropophilic population of Aedes aegypti mosquitoes in West Africa recently gave rise to American and Asian populations of this major disease vector
inferred← citeshttps://doi.org/10.1186/s12915-026-02578-8openalex-snapshot
Genomic signatures of speciation and adaptation in the ctenophore Mnemiopsis
inferred← citeshttps://doi.org/10.1186/s13059-016-0966-4openalex-snapshot
Disease vectors in the era of next generation sequencing
inferred← citeshttps://doi.org/10.1186/s13059-017-1346-4openalex-snapshot
The interplay of demography and selection during maize domestication and expansion
inferred← citeshttps://doi.org/10.1186/s13059-018-1528-8openalex-snapshot
Genomic approaches for studying crop evolution
inferred← citeshttps://doi.org/10.1186/s13059-020-02141-wopenalex-snapshot
Improved reference genome of the arboviral vector Aedes albopictus
inferred← citeshttps://doi.org/10.1186/s40168-022-01372-2openalex-snapshot
Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium
inferred← citeshttps://doi.org/10.1186/s40665-014-0009-xopenalex-snapshot
A framework for incorporating evolutionary genomics into biodiversity conservation and management
inferred← citeshttps://doi.org/10.12688/f1000research.104368.1openalex-snapshot
ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language
inferred← citeshttps://doi.org/10.12688/f1000research.104368.2openalex-snapshot
ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language
inferred← citeshttps://doi.org/10.12688/f1000research.104368.3openalex-snapshot
ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language
inferred← citeshttps://doi.org/10.13140/rg.2.2.17024.84488openalex-snapshot
The genetic basis for adaptation in natural populations
inferred← citeshttps://doi.org/10.1371/journal.pgen.1006529openalex-snapshot
A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy
inferred← citeshttps://doi.org/10.1371/journal.pgen.1007414openalex-snapshot
The complex geography of domestication of the African rice Oryza glaberrima
inferred← citeshttps://doi.org/10.1371/journal.pgen.1007672openalex-snapshot
The genomic basis of environmental adaptation in house mice
inferred← citeshttps://doi.org/10.1371/journal.pgen.1008119openalex-snapshot
Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change
inferred← citeshttps://doi.org/10.1371/journal.pgen.1009495openalex-snapshot
The genomics of rapid climatic adaptation and parallel evolution in North American house mice
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