Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

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Documentation for package ‘dartR.popgen’ version 1.0.0

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gl.blast Aligns nucleotides sequences against those present in a target database using blastn
gl.collapse Collapses a distance matrix by amalgamating populations with pairwise fixed difference count less that a threshold
gl.evanno Creates an Evanno plot from a STRUCTURE run object
gl.ld.distance Plots linkage disequilibrium against distance by population disequilibrium patterns
gl.ld.haplotype Visualize patterns of linkage disequilibrium and identification of haplotypes
gl.LDNe Estimates effective population size using the Linkage Disequilibrium method based on NeEstimator (V2)
gl.map.structure Maps a STRUCTURE plot using a genlight object
gl.nhybrids Creates an input file for the program NewHybrids and runs it if NewHybrids is installed
gl.outflank Identifies loci under selection per population using the outflank method of Whitlock and Lotterhos (2015)
gl.plot.faststructure Plots fastStructure analysis results (Q-matrix)
gl.plot.structure Plots STRUCTURE analysis results (Q-matrix)
gl.run.epos Run EPOS for Inference of Historical Population-Size Changes
gl.run.faststructure Runs a faststructure analysis using a genlight object
gl.run.stairway2 Run Stairway Plot 2 for Demographic History Inference
gl.run.structure Runs a STRUCTURE analysis using a genlight object
gl.sfs Creates a site frequency spectrum based on a dartR or genlight object
utils.outflank OutFLANK: An Fst outlier approach by Mike Whitlock and Katie Lotterhos, University of British Columbia.
utils.outflank.MakeDiploidFSTMat Creates OutFLANK input file from individual genotype info.
utils.outflank.plotter Plotting functions for Fst distributions after OutFLANK
utils.structure.evanno Util function for evanno plots
utils.structure.genind2gtypes structure util functions
utils.structure.run Utility function to run Structure