| gi2gl | Converts a genind object into a genlight object | 
| gl.alf | Calculates allele frequency of the first and second allele for each loci A very simple function to report allele frequencies | 
| gl.allele.freq | Generates percentage allele frequencies by locus and population | 
| gl.amova | Performs AMOVA using genlight data | 
| gl.assign.grm | Population assignment using grm | 
| gl.assign.mahalanobis | Assign an individual of unknown provenance to population based on Mahalanobis Distance | 
| gl.assign.pa | Eliminates populations as possible source populations for an individual of unknown provenance, using private alleles | 
| gl.assign.pca | Assign an individual of unknown provenance to population based on PCA | 
| gl.basic.stats | Calculates basic statistics for each loci (Hs, Ho, Fis etc.) | 
| gl.blast | Aligns nucleotides sequences against those present in a target database using blastn | 
| gl.check.verbosity | Checks the current global verbosity | 
| gl.check.wd | Checks the global working directory | 
| gl.collapse | Collapses a distance matrix by amalgamating populations with pairwise fixed difference count less that a threshold | 
| gl.colors | This is a helper function that supports the creation of color palettes for all plotting functions. | 
| gl.compliance.check | Checks a genlight object to see if it complies with dartR expectations and amends it to comply if necessary | 
| gl.costdistances | Calculates cost distances for a given landscape (resistance matrix) | 
| gl.define.pop | Defines a new population in a genlight object for specified individuals | 
| gl.diagnostics.hwe | Provides descriptive stats and plots to diagnose potential problems with Hardy-Weinberg proportions | 
| gl.diagnostics.sim | Comparing simulations against theoretical expectations | 
| gl.dist.ind | Calculates a distance matrix for individuals defined in a genlight object | 
| gl.dist.pop | Calculates a distance matrix for populations with SNP genotypes in a genlight object | 
| gl.drop.ind | Removes specified individuals from a dartR genlight object | 
| gl.drop.loc | Removes specified loci from a dartR genlight object | 
| gl.drop.pop | Removes specified populations from a dartR genlight object | 
| gl.edit.recode.ind | Creates or edits individual (=specimen) names, creates a recode_ind file and applies the changes to a genlight object | 
| gl.edit.recode.pop | Creates or edits and applies a population re-assignment table | 
| gl.evanno | Creates an Evanno plot from a STRUCTURE run object | 
| gl.fdsim | Estimates the rate of false positives in a fixed difference analysis | 
| gl.filter.allna | Filters loci that are all NA across individuals and/or populations with all NA across loci | 
| gl.filter.callrate | Filters loci or specimens in a genlight {adegenet} object based on call rate | 
| gl.filter.hamming | Filters loci based on pairwise Hamming distance between sequence tags | 
| gl.filter.heterozygosity | Filters individuals with average heterozygosity greater than a specified upper threshold or less than a specified lower threshold | 
| gl.filter.hwe | Filters loci that show significant departure from Hardy-Weinberg Equilibrium | 
| gl.filter.locmetric | Filters loci on the basis of numeric information stored in other$loc.metrics in a genlight {adegenet} object | 
| gl.filter.maf | Filters loci on the basis of minor allele frequency (MAF) in a genlight 'adegenet' object | 
| gl.filter.monomorphs | Filters monomorphic loci, including those with all NAs | 
| gl.filter.overshoot | Filters loci for which the SNP has been trimmed from the sequence tag along with the adaptor | 
| gl.filter.pa | Filters loci that contain private (and fixed alleles) between two populations | 
| gl.filter.parent.offspring | Filters putative parent offspring within a population | 
| gl.filter.rdepth | Filters loci based on counts of sequence tags scored at a locus (read depth) | 
| gl.filter.reproducibility | Filters loci in a genlight {adegenet} object based on average repeatability of alleles at a locus | 
| gl.filter.secondaries | Filters loci that represent secondary SNPs in a genlight object | 
| gl.filter.sexlinked | Filters loci that are sex linked | 
| gl.filter.taglength | Filters loci in a genlight {adegenet} object based on sequence tag length | 
| gl.fixed.diff | Generates a matrix of fixed differences and associated statistics for populations taken pairwise | 
| gl.fst.pop | Calculates a pairwise Fst values for populations in a genlight object | 
| gl.genleastcost | Performs least-cost path analysis based on a friction matrix | 
| gl.grm | Calculates an identity by descent matrix | 
| gl.grm.network | Represents a genomic relationship matrix (GRM) as a network | 
| gl.He | Estimates expected Heterozygosity | 
| gl.Ho | Estimates observed Heterozygosity | 
| gl.hwe.pop | Performs Hardy-Weinberg tests over loci and populations | 
| gl.ibd | Performs isolation by distance analysis | 
| gl.impute | Imputates missing data | 
| gl.install.vanilla.dartR | Installs all required packages for using all functions available in dartR | 
| gl.join | Combines two genlight objects | 
| gl.keep.ind | Removes all but the specified individuals from a dartR genlight object | 
| gl.keep.loc | Removes all but the specified loci from a genlight object | 
| gl.keep.pop | Removes all but the specified populations from a dartR genlight 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.list.reports | Prints dartR reports saved in tempdir | 
| gl.load | Loads an object from compressed binary format produced by gl.save() | 
| gl.make.recode.ind | Creates a proforma recode_ind file for reassigning individual (=specimen) names | 
| gl.make.recode.pop | Creates a proforma recode_pop_table file for reassigning population names | 
| gl.map.interactive | Creates an interactive map (based on latlon) from a genlight object | 
| gl.map.structure | Maps a STRUCTURE plot using a genlight object | 
| gl.merge.pop | Merges two or more populations in a genlight object into one population | 
| 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.pcoa | Ordination applied to genotypes in a genlight object (PCA), in an fd object, or to a distance matrix (PCoA) | 
| gl.pcoa.plot | Bivariate or trivariate plot of the results of an ordination generated using gl.pcoa() | 
| gl.percent.freq | Generates percentage allele frequencies by locus and population | 
| gl.play.history | Replays the history and applies it to a genlight object | 
| gl.plot.faststructure | Plots fastStructure analysis results (Q-matrix) | 
| gl.plot.heatmap | Represents a distance matrix as a heatmap | 
| gl.plot.network | Represents a distance or dissimilarity matrix as a network | 
| gl.plot.structure | Plots STRUCTURE analysis results (Q-matrix) | 
| gl.print.history | Prints history of a genlight object | 
| gl.print.reports | Prints dartR reports saved in tempdir | 
| gl.propShared | Calculates a similarity (distance) matrix for individuals on the proportion of shared alleles | 
| gl.random.snp | Randomly changes the allocation of 0's and 2's in a genlight object | 
| gl.read.csv | Reads SNP data from a csv file into a genlight object | 
| gl.read.dart | Imports DArT data into dartR and converts it into a dartR genlight object | 
| gl.read.fasta | Reads FASTA files and converts them to genlight object | 
| gl.read.silicodart | Imports presence/absence data from SilicoDArT to genlight {agegenet} format (ploidy=1) | 
| gl.read.vcf | Converts a vcf file into a genlight object | 
| gl.reassign.pop | Assigns an individual metric as pop in a genlight {adegenet} object | 
| gl.recalc.metrics | Recalculates locus metrics when individuals or populations are deleted from a genlight {adegenet} object | 
| gl.recode.ind | Recodes individual (=specimen = sample) labels in a genlight object | 
| gl.recode.pop | Recodes population assignments in a genlight object | 
| gl.rename.pop | Renames a population in a genlight object | 
| gl.report.bases | Reports summary of base pair frequencies | 
| gl.report.callrate | Reports summary of Call Rate for loci or individuals | 
| gl.report.diversity | Calculates diversity indexes for SNPs | 
| gl.report.fstat | Reports various statistics of genetic differentiation between populations with confident intervals | 
| gl.report.hamming | Calculates the pairwise Hamming distance between DArT trimmed DNA sequences | 
| gl.report.heterozygosity | Reports observed, expected and unbiased heterozygosities and FIS (inbreeding coefficient) by population or by individual from SNP data | 
| gl.report.hwe | Reports departure from Hardy-Weinberg proportions | 
| gl.report.ld.map | Calculates pairwise linkage disequilibrium by population | 
| gl.report.locmetric | Reports summary of the slot $other$loc.metrics | 
| gl.report.maf | Reports minor allele frequency (MAF) for each locus in a SNP dataset | 
| gl.report.monomorphs | Reports monomorphic loci | 
| gl.report.overshoot | Reports loci for which the SNP has been trimmed from the sequence tag along with the adaptor | 
| gl.report.pa | Reports private alleles (and fixed alleles) per pair of populations | 
| gl.report.parent.offspring | Identifies putative parent offspring within a population | 
| gl.report.rdepth | Reports summary of Read Depth for each locus | 
| gl.report.replicates | Identify replicated individuals | 
| gl.report.reproducibility | Reports summary of RepAvg (repeatability averaged over both alleles for each locus) or reproducibility (repeatability of the scores for fragment presence/absence) | 
| gl.report.secondaries | Reports loci containing secondary SNPs in sequence tags and calculates number of invariant sites | 
| gl.report.sexlinked | Identifies loci that are sex linked | 
| gl.report.taglength | Reports summary of sequence tag length across loci | 
| gl.run.faststructure | Runs a faststructure analysis using a genlight object | 
| gl.run.structure | Runs a STRUCTURE analysis using a genlight object | 
| gl.sample | Samples individuals from populations | 
| gl.save | Saves an object in compressed binary format for later rapid retrieval | 
| gl.select.colors | Selects colors from one of several palettes and output as a vector | 
| gl.select.shapes | Selects shapes from the base R shape palette and outputs as a vector | 
| gl.set.verbosity | Sets the default verbosity level | 
| gl.sfs | Creates a site frequency spectrum based on a dartR or genlight object | 
| gl.sim.create_dispersal | Creates a dispersal file as input for the function gl.sim.WF.run | 
| gl.sim.emigration | Simulates emigration between populations | 
| gl.sim.ind | Simulates individuals based on the allele frequencies provided via a genlight object. | 
| gl.sim.mutate | Simulates mutations within a genlight object | 
| gl.sim.offspring | Simulates a specified number of offspring based on alleles provided by potential father(s) and mother(s) | 
| gl.sim.WF.run | Runs Wright-Fisher simulations | 
| gl.sim.WF.table | Creates the reference table for running gl.sim.WF.run | 
| gl.smearplot | Smear plot of SNP or presence/absence (SilicoDArT) data | 
| gl.sort | re-sorts genlight objects | 
| gl.spatial.autoCorr | Spatial autocorrelation following Smouse and Peakall 1999 | 
| gl.subsample.loci | Subsamples n loci from a genlight object and return it as a genlight object | 
| gl.test.heterozygosity | Tests the difference in heterozygosity between populations taken pairwise | 
| gl.tree.nj | Outputs an nj tree to summarize genetic similarity among populations | 
| gl.write.csv | Writes out data from a genlight object to csv file | 
| gl2bayescan | Converts a genlight object into a format suitable for input to Bayescan | 
| gl2bpp | Converts a genlight object into a format suitable for input to the BPP program | 
| gl2dartR | Convert a genlight object to a dartR object | 
| gl2demerelate | Creates a dataframe suitable for input to package {Demerelate} from a genlight {adegenet} object | 
| gl2eigenstrat | Converts a genlight object into eigenstrat format | 
| gl2fasta | Concatenates DArT trimmed sequences and outputs a FASTA file | 
| gl2faststructure | Converts a genlight object into faststructure format (to run faststructure elsewhere) | 
| gl2gds | Converts a genlight object into gds format | 
| gl2genalex | Converts a genlight object into a format suitable for input to genalex | 
| gl2genepop | Converts a genlight object into genepop format (and file) | 
| gl2geno | Converts a genlight object to geno format from package LEA | 
| gl2gi | Converts a genlight object to genind object | 
| gl2hiphop | Converts a genlight objects into hiphop format | 
| gl2phylip | Creates a Phylip input distance matrix from a genlight (SNP) {adegenet} object | 
| gl2plink | Converts a genlight object into PLINK format | 
| gl2related | Converts a genlight object to format suitable to be run with Coancestry | 
| gl2sa | Converts genlight objects to the format used in the SNPassoc package | 
| gl2sfs | Converts a genlight object into a sfs input file | 
| gl2shp | Converts a genlight object to ESRI shapefiles or kml files | 
| gl2snapp | Converts a genlight object to nexus format suitable for phylogenetic analysis by SNAPP (via BEAUti) | 
| gl2structure | Converts a genlight object to STRUCTURE formatted files | 
| gl2svdquartets | Converts a genlight object to nexus format PAUP SVDquartets | 
| gl2treemix | Converts a genlight object to a treemix input file | 
| gl2vcf | Converts a genlight object into vcf format | 
| utils.assignment | Population assignment probabilities | 
| utils.assignment_2 | Population assignment probabilities | 
| utils.assignment_3 | Population assignment probabilities | 
| utils.assignment_4 | Population assignment probabilities | 
| utils.basic.stats | Calculates mean observed heterozygosity, mean expected heterozygosity and Fis per locus, per population and various population differentiation measures | 
| utils.check.datatype | Utility function to check the class of an object passed to a function | 
| utils.clumpp | Functions from package starmie for merging Q matrices from Structure runs using the CLUMPP algorithms. | 
| utils.dart2genlight | Converts DarT to genlight. | 
| utils.dist.binary | Calculates a distance matrix for individuals defined in a dartR genlight object using binary P/A data (SilicoDArT) | 
| utils.dist.ind.snp | Calculates a distance matrix for individuals defined in a dartR genlight object using SNP data (DArTseq) | 
| utils.flag.start | A utility script to flag the start of a script | 
| utils.hamming | Calculates the Hamming distance between two DArT trimmed DNA sequences | 
| utils.het.pop | Calculates expected mean expected heterozygosity per population | 
| utils.jackknife | Conducts jackknife resampling using a genlight object | 
| utils.n.var.invariant | A utility script to calculate the number of variant and invariant sites by locus | 
| 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.plot.save | An internal function to save a ggplot object to disk in RDS binary format | 
| utils.read.dart | utility function to read in DArT data | 
| utils.recalc.avgpic | A utility script to recalculate the OneRatioRef, OneRatioSnp, PICRef, PICSnp, and AvgPIC by locus after some individuals or populations have been deleted. | 
| utils.recalc.callrate | A utility script to recalculate the callrate by locus after some populations have been deleted | 
| utils.recalc.freqhets | A utility script to recalculate the frequency of the heterozygous SNPs by locus after some populations have been deleted | 
| utils.recalc.freqhomref | A utility script to recalculate the frequency of the homozygous reference SNP by locus after some populations have been deleted | 
| utils.recalc.freqhomsnp | A utility script to recalculate the frequency of the homozygous alternate SNP by locus after some populations have been deleted | 
| utils.recalc.maf | A utility script to recalculate the minor allele frequency by locus, typically after some populations have been deleted | 
| utils.reset.flags | A utility script to reset to FALSE (or TRUE) the locus metric flags after some individuals or populations have been deleted. | 
| utils.spautocor | Spatial autocorrelation coefficient calculations | 
| utils.structure.evanno | Util function for evanno plots | 
| utils.structure.genind2gtypes | structure util functions | 
| utils.structure.run | Utility function to run Structure |