Stacks: an analysis tool set for population genomics

Keywords

Population genomics, Genomics, Biology, Massively parallel, Software

References

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• Evolutionary and ecological functional genomicsMartin E. Feder, Thomas Mitchell‐Olds — 2003
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• A conserved haplotype controls parallel adaptation in geographically distant salmonid populationsMichael R. Miller, Joseph P. Brunelli, Paul Wheeler — 2012
• GENOMIC REGIONS WITH A HISTORY OF DIVERGENT SELECTION AFFECT FITNESS OF HYBRIDS BETWEEN TWO BUTTERFLY SPECIESZachariah Gompert, Lauren K. Lucas, Chris C. Nice — 2012
• Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samplesSimon Boitard, Robert Kofler, Pierre Françoise — 2013
• Rapid development of molecular markers by next-generation sequencing linked to a gene conferring phomopsis stem blight disease resistance for marker-assisted selection in lupin (Lupinus angustifolius L.) breedingHuaan Yang, Ye Tao, Zequn Zheng — 2012
• Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and WindowsLaurent Excoffier, Heidi E. L. Lischer — 2010
• PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled IndividualsRobert Kofler, Pablo Orozco‐terWengel, Nicola De Maio — 2011
• Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogasterRobert Kofler, Andrea J. Betancourt, Christian Schlötterer — 2012
• Inferring Phylogenies from RAD Sequence DataBenjamin E. Rubin, Richard H. Ree, Corrie S. Moreau — 2012
• Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing ReadsPaul D. Etter, Jessica Preston, Susan Bassham — 2011
• The effect of RAD allele dropout on the estimation of genetic variation within and between populationsMathieu Gautier, Karim Gharbi, Timothée Cezard — 2013

Cited by

• High‐throughput SNPs for all: genotyping‐in‐thousandsGonzález Olmedo, José Alberto — 2015
• Hybrid dynamics in a species group of swallowtail butterfliesMalcolm James McCusker — 2016
• Genomic islands of divergence linked to ecotypic variation in sockeye salmon健也 安尾 — 2017
• Adaptive capabilities and fitness consequences associated with pollution exposure in fishDaniel Dupuis — 2017
• Genomewide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids‐adapted clade of cichlids from the Congo RiverDave Taylor — 2017
• A GLABRA1 ortholog on LG A9 controls trichome number in the Japanese leafy vegetables Mizuna and Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey): evidence from QTL analysisSri Puspita Dewi — 2017
• Cis-Regulatory Evolution in a Wild Primate: Infection-Associated Genetic Variation Drives Differential Expression of MHC-DQA1 In-VitroMichel Crozier — 2017
• Distinct sources of gene flow produce contrasting population genetic dynamics at different range boundaries of a Choristoneura budworm英靖 近澤 — 2017
• Deriving genotypes from RAD-seq short-read data using StacksK. G. Serebrennicova, Е. П. Кузнецова, A. A Lapshikhin — 2017
• Patterns of genomic variation in Coho salmon following reintroduction to the interior Columbia RiverLuis Gonzalo Díez — 2017
• Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approachArne Jacobs, Michele De Noia, Kim Præbel — 2017
• Opposing patterns of intraspecific and interspecific differentiation in sex chromosomes and autosomesWenqi Zhou, Wenjing Duan — 2018
• Genetic Diversity in the UV Sex Chromosomes of the Brown Alga EctocarpusT. E. Browder — 2018
• Delimiting species of marine gastropods (Turridae, Conoidea) using RAD sequencing in an integrative taxonomy frameworkV. I. Unkovskii, G. A. VASIL'EVA, R. P. EVSTIGNEEVA — 2018
• Genomic insights into the vulnerability of sympatric whitefish species flocksElena Vozmediano — 2019
• Unexpected population fragmentation in an endangered seabird: the case of the Peruvian diving-petrelJosé Antonio Carazo Muriel — 2019
• A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals洋史 冨田 — 2019
• Development of Single Nucleotide Polymorphism (SNP) Markers for Analysis of Population Structure and Invasion Pathway in the Coconut Leaf Beetle Brontispa longissima (Gestro) Using Restriction Site-Associated DNA (RAD) Genotyping in Southern ChinaLozano de Vílchez, Enriqueta — 2020
• A Method for Reference-Free Genome Assembly Quality AssessmentJoshua Burkhart — 2013
• Statistical and Comparative Phylogeography of Mexican Freshwater Taxa in Extreme Aquatic EnvironmentsLyndon M. Coghill — 2013

Related papers

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• Population Genomics of Fungal and Oomycete Pathogens.Niklaus J. Grünwald, Bruce A. McDonald, Michael G. Milgroom — 2016
• Harnessing population genomics to understand how bacterial pathogens emerge, adapt to crop hosts, and disseminate.Boris A. Vinatzer, Caroline Monteil, Christopher R. Clarke — 2014
• Population genomics: a new generation of genome scans to bridge the gap with functional genomicsAurélie Bonin — 2008
• Research progress of plant population genomics based on high-throughput sequencing.Yunsheng Wang — 2016