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PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

https://doi.org/10.1371/journal.pone.0015925

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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De novo transcriptome assembly with ABySS

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VarScan: variant detection in massively parallel sequencing of individual and pooled samples

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A probabilistic framework for aligning paired-end RNA-seq data

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Testing hypotheses of a coevolutionary key innovation reveals a complex suite of traits involved in defusing the mustard oil bomb

inferred← citeshttps://doi.org/10.1080/00218839.2025.2455852openalex-snapshot

Standard methods and good practices in Apis honey bee omics research

inferred← citeshttps://doi.org/10.1086/731996openalex-snapshot

Defense Heterogeneity in Host Populations Gives Rise to Pathogen Diversity

inferred← citeshttps://doi.org/10.1093/bfgp/elv010openalex-snapshot

Beyond fruit-flies: population genomic advances in non-Drosophila arthropods

inferred← citeshttps://doi.org/10.1093/bioinformatics/btae508openalex-snapshot

grenedalf: population genetic statistics for the next generation of pool sequencing

inferred← citeshttps://doi.org/10.1093/bioinformatics/btr589openalex-snapshot

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

inferred← citeshttps://doi.org/10.1093/bioinformatics/btr691openalex-snapshot

PopDrowser: the Population Drosophila Browser

inferred← citeshttps://doi.org/10.1093/bioinformatics/btv449openalex-snapshot

SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data

inferred← citeshttps://doi.org/10.1093/cz/zow067openalex-snapshot

Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies

inferred← citeshttps://doi.org/10.1093/etojnl/vgag010openalex-snapshot

Beyond acute toxicity: evolutionary response by rapid polygenic adaptation to a complex environmental stressor in Chironomus riparius

inferred← citeshttps://doi.org/10.1093/evlett/qrad039openalex-snapshot

Parental care shapes the evolution of molecular genetic variation

inferred← citeshttps://doi.org/10.1093/evlett/qrae047openalex-snapshot

Selection on the vascular-remodeling BMPER gene is associated with altitudinal adaptation in an insular lizard

inferred← citeshttps://doi.org/10.1093/evolut/qpaf148openalex-snapshot

Genetic consequences of gene surfing and their relationship to fitness

inferred← citeshttps://doi.org/10.1093/evolut/qpag110openalex-snapshot

Museum genomics links MC1R alleles to adaptive winter coat color polymorphism in the long-tailed weasel

inferred← citeshttps://doi.org/10.1093/g3journal/jkab045openalex-snapshot

Complex pleiotropic genetic architecture of evolved heat stress and oxidative stress resistance in the nematode Caenorhabditis remanei

inferred← citeshttps://doi.org/10.1093/g3journal/jkab286openalex-snapshot

A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridizing fire-bellied toads ( Bombina bombina and Bombina variegata )

inferred← citeshttps://doi.org/10.1093/g3journal/jkac270openalex-snapshot

Draft genome and multi-tissue transcriptome assemblies of the Neotropical leaf-frog Phyllomedusa bahiana

inferred← citeshttps://doi.org/10.1093/g3journal/jkaf269openalex-snapshot

The missing data problem in population genomics and statistical methods to address them

inferred← citeshttps://doi.org/10.1093/gbe/evaa206openalex-snapshot

The Evolution of Phenotypic Plasticity in Response to Temperature Stress

inferred← citeshttps://doi.org/10.1093/gbe/evaa234openalex-snapshot

Selective Sweeps in a Nutshell: The Genomic Footprint of Rapid Insecticide Resistance Evolution in the Almond Agroecosystem

inferred← citeshttps://doi.org/10.1093/gbe/evab031openalex-snapshot

Transposable Element Landscape in Drosophila Populations Selected for Longevity

inferred← citeshttps://doi.org/10.1093/gbe/evab053openalex-snapshot

The Genome of the Margined White Butterfly (Pieris macdunnoughii): Sex Chromosome Insights and the Power of Polishing with PoolSeq Data

inferred← citeshttps://doi.org/10.1093/gbe/evab121openalex-snapshot

Characterization of a Sex-Determining Region and Its Genomic Context via Statistical Estimates of Haplotype Frequencies in Daughters and Sons Sequenced in Pools

inferred← citeshttps://doi.org/10.1093/gbe/evac030openalex-snapshot

Selection of Genome-Wide SNPs for Pooled Allelotyping Assays Useful for Population Monitoring

inferred← citeshttps://doi.org/10.1093/gbe/evad113openalex-snapshot

Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila pseudoobscura

inferred← citeshttps://doi.org/10.1093/gbe/evad138openalex-snapshot

Potential Contribution of Ancient Introgression to the Evolution of a Derived Reproductive Strategy in Ricefishes

inferred← citeshttps://doi.org/10.1093/gbe/evad168openalex-snapshot

Contrasting Evolutionary Patterns Between Sexual and Asexual Lineages in a Genomic Region Linked to Reproductive Mode Variation in the pea aphid

inferred← citeshttps://doi.org/10.1093/gbe/evae006openalex-snapshot

Chromosome-Level Assembly of Artemia franciscana Sheds Light on Sex Chromosome Differentiation

inferred← citeshttps://doi.org/10.1093/gbe/evae217openalex-snapshot

Genetic Variation in Jamaican Populations of the Coffee Berry Borer, Hypothenemus hampei

inferred← citeshttps://doi.org/10.1093/gbe/evag083openalex-snapshot

Genomic Patterns of Parallel Divergence Across Demographically Heterogeneous Stickleback Populations in Eastern Canada

inferred← citeshttps://doi.org/10.1093/gbe/evag132openalex-snapshot

PolyAdapt : Characterizing Polygenic Adaptive Architectures in the Presence of Strong Linkage Disequilibrium

inferred← citeshttps://doi.org/10.1093/gbe/evag151openalex-snapshot

Experimental Evolution Under Biased Sex Ratios: Phenotypic and Genomic Responses in the Bulb Mite, Rhizoglyphus robini

inferred← citeshttps://doi.org/10.1093/gbe/evu085openalex-snapshot

Population-Genetic Inference from Pooled-Sequencing Data

inferred← citeshttps://doi.org/10.1093/gbe/evu229openalex-snapshot

Faster-X Effects in Two Drosophila Lineages

inferred← citeshttps://doi.org/10.1093/gbe/evw094openalex-snapshot

Pooled Enrichment Sequencing Identifies Diversity and Evolutionary Pressures at NLR Resistance Genes within a Wild Tomato Population

inferred← citeshttps://doi.org/10.1093/gbe/evw095openalex-snapshot

Genomic Signatures of Speciation in Sympatric and Allopatric Hawaiian Picture-WingedDrosophila

inferred← citeshttps://doi.org/10.1093/gbe/evw291openalex-snapshot

Variation in the intensity of selection on codon bias over time causes contrasting patterns of base composition evolution in Drosophila

inferred← citeshttps://doi.org/10.1093/gbe/evy004openalex-snapshot

Elevated Proportions of Deleterious Genetic Variation in Domestic Animals and Plants

inferred← citeshttps://doi.org/10.1093/gbe/evy015openalex-snapshot

Disentangling the Causes for Faster-X Evolution in Aphids

inferred← citeshttps://doi.org/10.1093/gbe/evz191openalex-snapshot

Balancing Selection Drives the Maintenance of Genetic Variation in Drosophila Antimicrobial Peptides

inferred← citeshttps://doi.org/10.1093/genetics/iyac037openalex-snapshot

Novel genetic basis of resistance to Bt toxin Cry1Ac in Helicoverpa zea

inferred← citeshttps://doi.org/10.1093/genetics/iyad050openalex-snapshot

Complexities of recapitulating polygenic effects in natural populations: replication of genetic effects on wing shape in artificially selected and wild-caught populations of Drosophila melanogaster

inferred← citeshttps://doi.org/10.1093/genetics/iyag068openalex-snapshot

The illusion of polygenicity in pool-seq genetic mapping studies: insufficient power can mask simple genetic architectures

inferred← citeshttps://doi.org/10.1093/icb/icac098openalex-snapshot

Population Genomic Time Series Data of a Natural Population Suggests Adaptive Tracking of Fluctuating Environmental Changes

inferred← citeshttps://doi.org/10.1093/jas/skaa229openalex-snapshot

Genomic diversity revealed by whole-genome sequencing in three Danish commercial pig breeds

inferred← citeshttps://doi.org/10.1093/jeb/voaf153openalex-snapshot

Expression of heat shock proteins and thermal sensitivity of male fertility across six Drosophila species

inferred← citeshttps://doi.org/10.1093/jhered/esae046openalex-snapshot

Genomic implications of the repeated shift to self-fertilization across a species’ geographic distribution

inferred← citeshttps://doi.org/10.1093/jhered/est005openalex-snapshot

Estimating the Population Mutation Rate from ade novoAssembled Bactrian Camel Genome and Cross-Species Comparison with Dromedary ESTs

inferred← citeshttps://doi.org/10.1093/jhered/esx115openalex-snapshot

Using Pool-seq to Search for Genomic Regions Affected by Hybrid Inviability in the copepod T. californicus

inferred← citeshttps://doi.org/10.1093/jhered/esz048openalex-snapshot

Elevated Heterozygosity in Adults Relative to Juveniles Provides Evidence of Viability Selection on Eagles and Falcons

inferred← citeshttps://doi.org/10.1093/jhered/esz056openalex-snapshot

Repeatability of Adaptive Radiation Depends on Spatial Scale: Regional Versus Global Replicates of Stickleback in Lake Versus Stream Habitats

inferred← citeshttps://doi.org/10.1093/molbev/msaa110openalex-snapshot

Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum

inferred← citeshttps://doi.org/10.1093/molbev/msaa120openalex-snapshot

Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

inferred← citeshttps://doi.org/10.1093/molbev/msaa227openalex-snapshot

Ecological Load and Balancing Selection in Circumboreal Barnacles

inferred← citeshttps://doi.org/10.1093/molbev/msab061openalex-snapshot

The Genomic Architecture of Adaptation to Larval Malnutrition Points to a Trade-off with Adult Starvation Resistance in Drosophila

inferred← citeshttps://doi.org/10.1093/molbev/msab155openalex-snapshot

The Worldwide Invasion of Drosophila suzukii Is Accompanied by a Large Increase of Transposable Element Load and a Small Number of Putatively Adaptive Insertions

inferred← citeshttps://doi.org/10.1093/molbev/msab177openalex-snapshot

Museomics Dissects the Genetic Basis for Adaptive Seasonal Coloration in the Least Weasel

inferred← citeshttps://doi.org/10.1093/molbev/msab259openalex-snapshot

Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource

inferred← citeshttps://doi.org/10.1093/molbev/msab368openalex-snapshot

A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population

inferred← citeshttps://doi.org/10.1093/molbev/msad068openalex-snapshot

High Nucleotide Diversity Accompanies Differential DNA Methylation in Naturally Diverging Populations

inferred← citeshttps://doi.org/10.1093/molbev/msae128openalex-snapshot

Genome-Wide Allele Frequency Changes Reveal That Dynamic Metapopulations Evolve Differently

inferred← citeshttps://doi.org/10.1093/molbev/msaf132openalex-snapshot

Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource

inferred← citeshttps://doi.org/10.1093/molbev/msaf251openalex-snapshot

Genomic Drivers of Pyrethroid Resistance Escalation in the Malaria Vector Anopheles funestus Across Africa

inferred← citeshttps://doi.org/10.1093/molbev/msr265openalex-snapshot

Late-Replicating Domains Have Higher Divergence and Diversity in Drosophila melanogaster

inferred← citeshttps://doi.org/10.1093/molbev/mst016openalex-snapshot

Maximum Likelihood Estimation of Frequencies of Known Haplotypes from Pooled Sequence Data

inferred← citeshttps://doi.org/10.1093/molbev/mst205openalex-snapshot

Massive Habitat-Specific Genomic Response in D. melanogaster Populations during Experimental Evolution in Hot and Cold Environments

inferred← citeshttps://doi.org/10.1093/molbev/mst221openalex-snapshot

A Guide for the Design of Evolve and Resequencing Studies

inferred← citeshttps://doi.org/10.1093/molbev/msu056openalex-snapshot

The Relation between Recombination Rate and Patterns of Molecular Evolution and Variation in Drosophila melanogaster

inferred← citeshttps://doi.org/10.1093/molbev/msu320openalex-snapshot

Patterns of Linkage Disequilibrium and Long Range Hitchhiking in Evolving Experimental Drosophila melanogaster Populations

inferred← citeshttps://doi.org/10.1093/molbev/msv120openalex-snapshot

Temperature-Related Reaction Norms of Gene Expression: Regulatory Architecture and Functional Implications

inferred← citeshttps://doi.org/10.1093/molbev/msv160openalex-snapshot

Evolutionary Transition from Pathogenicity to Commensalism: Global Regulator Mutations Mediate Fitness Gains through Virulence Attenuation

inferred← citeshttps://doi.org/10.1093/molbev/msv208openalex-snapshot

Parallelism and Epistasis in Skeletal Evolution Identified through Use of Phylogenomic Mapping Strategies

inferred← citeshttps://doi.org/10.1093/molbev/msw016openalex-snapshot

Genomic Evidence for Adaptive Inversion Clines inDrosophila melanogaster

inferred← citeshttps://doi.org/10.1093/molbev/msw282openalex-snapshot

Genomics of Parallel Experimental Evolution in Drosophila

inferred← citeshttps://doi.org/10.1093/molbev/msx188openalex-snapshot

Intrahost Genetic Diversity of Bacterial Symbionts Exhibits Evidence of Mixed Infections and Recombinant Haplotypes

inferred← citeshttps://doi.org/10.1093/molbev/msx247openalex-snapshot

Different Genomic Changes Underlie Adaptive Evolution in Populations of Contrasting History

inferred← citeshttps://doi.org/10.1093/molbev/msy003openalex-snapshot

Accumulation of Mutational Load at the Edges of a Species Range

inferred← citeshttps://doi.org/10.1093/molbev/msz029openalex-snapshot

Parallel Speciation of Wild Rice Associated with Habitat Shifts

inferred← citeshttps://doi.org/10.1093/molbev/msz076openalex-snapshot

Different Genomic Changes Underlie Adaptive Evolution in Populations of Contrasting History

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