ArticleMolecular ecology resources2013
Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples.
Article in Molecular ecology resources, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
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- Population Genomics of Two Closely Related Anhydrobiotic Midges Reveals Differences in Adaptation to Extreme Desiccation.Genome biology and evolution · 2023Article
- Genomic selection pressure discovery using site-frequency spectrum and reduced local variability statistics in Pakistani Dera-Din-Panah goat.Tropical animal health and production · 2023Article
- Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics modelPeerJ · 2022Article
- A brief history and popularity of methods and tools used to estimate micro-evolutionary forces.Ecology and evolution · 2021Review
- Museomics Dissects the Genetic Basis for Adaptive Seasonal Coloration in the Least Weasel.Molecular biology and evolution · 2021Article
- Population genomics of invasive rodents on islands: Genetic consequences of colonization and prospects for localized synthetic gene drive.Evolutionary applications · 2021Article
- Nuclear eDNA estimates population allele frequencies and abundance in experimental mesocosms and field samples.Molecular ecology · 2021Article
- Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses.Molecular biology and evolution · 2020Article
- Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations.Genome biology and evolution · 2020Article
- The quail genome: insights into social behaviour, seasonal biology and infectious disease response.BMC biology · 2020Article
- Population-level inferences from environmental DNA-Current status and future perspectives.Evolutionary applications · 2020Review
- Analysis of genome-wide SNPs based on 2b-RAD sequencing of pooled samples reveals signature of selection in different populations ofJournal of biosciences · 2019Article
- A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes.Molecular ecology resources · 2019Article
- Genomic divergence and adaptive convergence inProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Small and genetically highly structured populations in a long-legged bee, Rediviva longimanus, as inferred by pooled RAD-seq.BMC evolutionary biology · 2018Article
- Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus.Nature communications · 2018Article
- Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates.Nature communications · 2017Article
- Nucleotide diversity inflation as a genome-wide response to experimental lifespan extension in Drosophila melanogaster.BMC genomics · 2017Article
- Genome-wide analysis of long-term evolutionary domestication in Drosophila melanogaster.Scientific reports · 2016Article
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6 authors.
Funding
Abstract
Due to its cost effectiveness, next generation sequencing of pools of individuals (Pool-Seq) is becoming a popular strategy for genome-wide estimation of allele frequencies in population samples. As the allele frequency spectrum provides information about past episodes of selection, Pool-seq is also a promising design for genomic scans for selection. However, no software tool has yet been developed for selection scans based on Pool-Seq data. We introduce Pool-hmm, a Python program for the estimation of allele frequencies and the detection of selective sweeps in a Pool-Seq sample. Pool-hmm includes several options that allow a flexible analysis of Pool-Seq data, and can be run in parallel on several processors. Source code and documentation for Pool-hmm is freely available at https://qgsp.jouy.inra.fr/.
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