Cited by 815Genetic diversity and population structureGenomics and Phylogenetic StudiesGenetic Mapping and Diversity in Plants and Animals

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

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Kofler, Robert, Pandey, Ram Vinay, Schlötterer, Christian·2011·Bioinformatics

DOI 10.1093/bioinformatics/btr589PMC PMC3232374

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Abstract

SUMMARY: Sequencing pooled DNA samples (Pool-Seq) is the most cost-effective approach for the genome-wide comparison of population samples. Here, we introduce PoPoolation2, the first software tool specifically designed for the comparison of populations with Pool-Seq data. PoPoolation2 implements a range of commonly used measures of differentiation (F(ST), Fisher's exact test and Cochran-Mantel-Haenszel test) that can be applied on different scales (windows, genes, exons, SNPs). The result may be visualized with the widely used Integrated Genomics Viewer. AVAILABILITY AND IMPLEMENTATION: PoPoolation2 is implemented in Perl and R. It is freely available on http://code.google.com/p/popoolation2/ CONTACT: christian.schloetterer@vetmeduni.ac.at SUPPLEMENTARY INFORMATION: Manual: http://code.google.com/p/popoolation2/wiki/Manual Test data and tutorial: http://code.google.com/p/popoolation2/wiki/Tutorial Validation: http://code.google.com/p/popoolation2/wiki/Validation.

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Authors: Kofler, R., Pandey, R. V., & Schlötterer, C.
Affiliations: University of Veterinary Medicine Vienna (AT)
Corresponding author: Schlötterer, Christian
ORCID: Kofler, Robert
Pandey, Ram Vinay
Schlötterer, Christian
Venue: Bioinformatics
Publisher: Oxford University Press (OUP)
Published: 2011-10-23
Volume: 27
Issue: 24
Pages: 3435-3436
ISSN: 1367-4803 (ISSN-L)
1367-4811
DOI: 10.1093/bioinformatics/btr589
PMC: PMC3232374
OpenAlex: W2161950199
Cited by: 815
References: 23
Citations by year: 2026: 44 · 2025: 48 · 2024: 68 · 2023: 54 · 2022: 86 · 2021: 83 · 2020: 88 · 2019: 77 · 2018: 64 · 2017: 54 · 2016: 62 · 2015: 34 · 2014: 22 · 2013: 26 · 2012: 2
FWCI: 9.98
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by-nc
creativecommons.org/licenses/by-nc/3.0 (vor, 1806 d)
Locations: Bioinformatics (publishedVersion, cc-by-nc)
Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
HighWire Press Open Archive (submittedVersion)
Funders: Austrian Science Fund (P 22725, P19467)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Keywords: pooled DNA sequencing, genetic differentiation, F(ST), Fisher's exact test, Cochran-Mantel-Haenszel test, population genetics software
MeSH terms: Animals, Drosophila melanogaster, Genetics, Population, Software, Arabidopsis, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Genomics

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

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