AllopolyTutorialData    Simulated Allotetraploid Data
Bruvo.distance          Genetic Distance Metric of Bruvo et al.
Bruvo2.distance         Distance Measure of Bruvo et al. under Genome
                        Loss and Addition
FCRinfo                 Additional Data on Rubus Samples
G                       Internal Functions in polysat
Lynch.distance          Calculate Band-Sharing Dissimilarity Between
                        Genotypes
PIC                     Polymorphic Information Content
Samples                 Accessor and Replacement Functions for
                        "gendata" Objects
alleleCorrelations      Assign Alleles to Isoloci Based on Distribution
                        of Genotypes
alleleDiversity         Retrieve and Count Unique Alleles
assignClones            Group Individuals Based on a Distance Threshold
calcPopDiff             Estimate Population Differentiation Statistics
catalanAlleles          Sort Alleles into Isoloci
deSilvaFreq             Estimate Allele Frequencies with EM Algorithm
deleteSamples           Remove Samples or Loci from an Object
editGenotypes           Edit Genotypes Using the Data Editor
estimatePloidy          Estimate Ploidies Based on Allele Counts
find.missing.gen        Find Missing Genotypes
freq.to.genpop          Convert Allele Frequencies for Adegenet
genIndex                Find All Unique Genotypes for a Locus
genambig-class          Class "genambig"
genambig.to.genbinary   Convert Between Genotype Object Classes
genbinary-class         Class "genbinary"
gendata-class           Class "gendata"
gendata.to.genind       Convert Data to genind Format
genotypeDiversity       Genotype Diversity Statistics
genotypeProbs           Calculate Probabilities of Unambiguous
                        Genotypes
isMissing               Determine Whether Genotypes Are Missing
meandist.from.array     Tools for Working With Pairwise Distance Arrays
meandistance.matrix     Mean Pairwise Distance Matrix
merge-methods           Merge Two Genotype Objects into One
mergeAlleleAssignments
                        Merge Allele Assignment Matrices
pld                     Accessor, Replacement, and Manipulation
                        Functions for '"ploidysuper"' Objects
ploidysuper-class       Class '"ploidysuper"' and Subclasses
plotSSAllo              Perform Allele Assignments across Entire
                        Dataset
read.ATetra             Read File in ATetra Format
read.GeneMapper         Read GeneMapper Genotypes Tables
read.GenoDive           Import Genotype Data from GenoDive File
read.POPDIST            Read Genotype Data in POPDIST Format
read.SPAGeDi            Read Genotypes in SPAGeDi Format
read.STRand             Read Genotypes Produced by STRand Software
read.Structure          Read Genotypes and Other Data from a Structure
                        File
read.Tetrasat           Read Data from a TETRASAT Input File
recodeAllopoly          Create a New 'genambig' Dataset with Loci Split
                        into Isoloci
reformatPloidies        Convert Ploidy Format of a Dataset
simAllopoly             Generate Simulated Datasets
simgen                  Randomly Generated Data for Learning polysat
simpleFreq              Simple Allele Frequency Estimator
testgenotypes           Rubus Genotype Data for Learning polysat
viewGenotypes           Print Genotypes to the Console
write.ATetra            Write Genotypes in ATetra Format
write.GeneMapper        Write Genotypes to a Table Similarly to ABI
                        GeneMapper
write.GenoDive          Write a File in GenoDive Format
write.POPDIST           Write Genotypes to a POPDIST File
write.SPAGeDi           Write Genotypes in SPAGeDi Format
write.Structure         Write Genotypes in Structure 2.3 Format
write.Tetrasat          Write Genotype Data in Tetrasat Format
write.freq.SPAGeDi      Create a File of Allele Frequencies for SPAGeDi
