ArticleBMC bioinformatics2008
AWclust: point-and-click software for non-parametric population structure analysis.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 1 of them a synthesis that pooled it.
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Who cites it
38 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Optimizing phenotypic data analysis strategies to enhance genomic prediction in winter wheat breeding.Frontiers in plant science · 2026Article
- Advances in Whole Genome Sequencing: Methods, Tools, and Applications in Population Genomics.International journal of molecular sciences · 2025Review
- Article
- Genetic diversity of a Silybum marianum (L.) Gaertn. germplasm collection revealed by DNA Diversity Array Technology (DArTseq).PloS one · 2024Article
- Limited population genetic variation but pronounced seascape genetic structuring in populations of the Mediterranean mussel (Ecology and evolution · 2023Article
- Detection and distribution of two dominant alleles associated with the sweet kernel phenotype in almond cultivated germplasm.Frontiers in plant science · 2023Article
- Genotyping-by-Sequencing Defines Genetic Structure within the "Acquaviva" Red Onion Landrace.Plants (Basel, Switzerland) · 2022Article
- Review
- Hopping or Jumping on the Cliffs: The Unusual Phylogeographical and Demographic Structure of an Extremely Narrow Endemic Mediterranean Plant.Frontiers in plant science · 2021Article
- Article
- ddRAD sequencing-based genotyping for population structure analysis in cultivated tomato provides new insights into the genomic diversity of Mediterranean 'da serbo' type long shelf-life germplasm.Horticulture research · 2020Article
- A different view on fine-scale population structure in Western African populations.Human genetics · 2020Article
- Hitchhiking the high seas: Global genomics of rafting crabs.Ecology and evolution · 2019Article
- Genotyping by Sequencing of Cultivated Lentil (Frontiers in genetics · 2019Article
- GBS-derived SNP catalogue unveiled wide genetic variability and geographical relationships of Italian olive cultivars.Scientific reports · 2018Article
- Nonparametric approaches for population structure analysis.Human genomics · 2018Review
- Deciphering the sexual diploid members of thePhytoKeys · 2018Article
- Exploring Overlaps Between the Genomic and Environmental Determinants of LVH and Stroke: A Multicenter Study in West Africa.Global heart · 2017Article
- Transferability of genome-wide associated loci for asthma in African Americans.The Journal of asthma : official journal of the Association for the Care of Asthma · 2017Article
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2 authors.
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Abstract
backgroundPopulation structure analysis is important to genetic association studies and evolutionary investigations. Parametric approaches, e.g. STRUCTURE and L-POP, usually assume Hardy-Weinberg equilibrium (HWE) and linkage equilibrium among loci in sample population individuals. However, the assumptions may not hold and allele frequency estimation may not be accurate in some data sets. The improved version of STRUCTURE (version 2.1) can incorporate linkage information among loci but is still sensitive to high background linkage disequilibrium. Nowadays, large-scale single nucleotide polymorphisms (SNPs) are becoming popular in genetic studies. Therefore, it is imperative to have software that makes full use of these genetic data to generate inference even when model assumptions do not hold or allele frequency estimation suffers from high variation.
resultsWe have developed point-and-click software for non-parametric population structure analysis distributed as an R package. The software takes advantage of the large number of SNPs available to categorize individuals into ethnically similar clusters and it does not require assumptions about population models. Nor does it estimate allele frequencies. Moreover, this software can also infer the optimal number of populations.
conclusionOur software tool employs non-parametric approaches to assign individuals to clusters using SNPs. It provides efficient computation and an intuitive way for researchers to explore ethnic relationships among individuals. It can be complementary to parametric approaches in population structure analysis.
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