Journal ArticleDOI
genalex 6: genetic analysis in Excel. Population genetic software for teaching and research
Rodney Peakall,Peter E. Smouse +1 more
TLDR
Genalex is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data.Abstract:
genalex is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency-based analyses include heterozygosity, F statistics, Nei's genetic distance, population assignment, probabilities of identity and pairwise relatedness. Distance-based calculations include amova, principal coordinates analysis (PCA), Mantel tests, multivariate and 2D spatial autocorrelation and twogener. More than 20 different graphs summarize data and aid exploration. Sequence and genotype data can be imported from automated sequencers, and exported to other software. Initially designed as tool for teaching, genalex 6 now offers features for researchers as well. Documentation and the program are available at http://www.anu.edu.au/BoZo/GenAlEx/read more
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GenAlEx 6.5
Rod Peakall,Peter E. Smouse +1 more
TL;DR: GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel that offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences.
Journal ArticleDOI
Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction.
TL;DR: The R package poppr is developed providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations, and functions for genotypic diversity and clone censoring are specific for clonal populations.
Journal ArticleDOI
Ancient Admixture in Human History
Nick Patterson,Priya Moorjani,Yontao Luo,Swapan Mallick,Nadin Rohland,Yiping Zhan,Teri Genschoreck,Teresa Webster,David Reich,David Reich +9 more
TL;DR: A suite of methods for learning about population mixtures are presented, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture.
Journal ArticleDOI
fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets
TL;DR: Developing efficient algorithms for approximate inference of the model underlying the STRUCTURE program using a variational Bayesian framework and proposing useful heuristic scores to identify the number of populations represented in a data set and a new hierarchical prior to detect weak population structure in the data.
Journal ArticleDOI
A chromosome conformation capture ordered sequence of the barley genome
Martin Mascher,Heidrun Gundlach,Axel Himmelbach,Sebastian Beier,Sven Twardziok,Thomas Wicker,Volodymyr Radchuk,Christoph Dockter,Pete E. Hedley,Joanne Russell,Micha Bayer,Luke Ramsay,Hui Liu,Georg Haberer,Xiao-Qi Zhang,Qisen Zhang,Roberto A. Barrero,Lin Li,Stefan Taudien,Marco Groth,Marius Felder,Alex Hastie,Hana Šimková,Helena Staňková,Jan Vrána,Saki Chan,María Muñoz-Amatriaín,Rachid Ounit,Steve Wanamaker,Dan Bolser,Christian Colmsee,Thomas Schmutzer,Lala Aliyeva-Schnorr,Stefano Grasso,Jaakko Tanskanen,Anna Chailyan,Dharanya Sampath,Darren Heavens,Leah Clissold,Sujie Cao,Brett Chapman,Fei Dai,Yong Han,Hua Li,Xuan Li,Chongyun Lin,John K. McCooke,Cong Tan,Penghao Wang,Songbo Wang,Shuya Yin,Gaofeng Zhou,Jesse Poland,Matthew I. Bellgard,Ljudmilla Borisjuk,Andreas Houben,Jaroslav Doležel,Sarah Ayling,Stefano Lonardi,Paul J. Kersey,Peter Langridge,Gary J. Muehlbauer,Matthew D. Clark,Matthew D. Clark,Mario Caccamo,Mario Caccamo,Alan H. Schulman,Klaus F. X. Mayer,Matthias Platzer,Timothy J. Close,Uwe Scholz,Mats Hansson,Guoping Zhang,Ilka Braumann,Manuel Spannagl,Chengdao Li,Chengdao Li,Chengdao Li,Robbie Waugh,Robbie Waugh,Nils Stein,Nils Stein +81 more
TL;DR: The importance of the barley reference sequence for breeding is demonstrated by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
References
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Journal ArticleDOI
Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.
TL;DR: In this article, a framework for the study of molecular variation within a single species is presented, where information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes.
Journal Article
Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.
Journal ArticleDOI
Estimating relatedness using genetic markers.
TL;DR: A new method is described for estimating genetic relatedness from genetic markers such as protein polymorphisms based on Grafen's (1985) relatedness coefficient, which eliminates a downward bias for small sample sizes and improves estimation of relatedness for subsets of population samples.
Journal ArticleDOI
Multiple regression and correlation extensions of the mantel test of matrix correspondence
TL;DR: The Mantel test as discussed by the authors is one of the most widely used matrix correlation measures in population biology and has been widely applied in geography and psychometrics (Hubert, 1979a, b).
Journal ArticleDOI
Microsatellite analysis of population structure in Canadian polar bears.
TL;DR: Using eight hypervariable microsatellite loci to study the genetic relationships between four Canadian polar bear populations indicates that gene flow between local populations is restricted despite the long‐distance seasonal movements undertaken by polar bears.
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