$,genind-method         Accessors for adegenet objects
.internal_C_routines    Internal C routines
AIC.snapclust           Compute Akaike Information Criterion (AIC) for
                        snapclust
AICc                    Compute Akaike Information Criterion for small
                        samples (AICc) for snapclust
BIC.snapclust           Compute Bayesian Information Criterion (BIC)
                        for snapclust
DNAbin2genind           Importing data from an alignement of sequences
                        to a genind object
H3N2                    Seasonal influenza (H3N2) HA segment data
HWE.test.genind         Hardy-Weinberg Equilibrium test for multilocus
                        data
Hs                      Expected heterozygosity (Hs)
Hs.test                 Test differences in expected heterozygosity
                        (Hs)
KIC                     Compute Akaike Information Criterion for small
                        samples (AICc) for snapclust
SNPbin-class            Formal class "SNPbin"
a.score                 Compute and optimize a-score for Discriminant
                        Analysis of Principal Components (DAPC)
adegenet.package        The adegenet package
adegenetServer          Web servers for adegenet
adegenetWeb             Functions to access online resources for
                        adegenet
as-method               Converting genind/genpop objects to other
                        classes
as.SNPbin               Conversion to class "SNPbin"
as.genlight             Conversion to class "genlight"
checkType               Auxiliary functions for adegenet
chooseCN                Function to choose a connection network
colorplot               Represents a cloud of points with colors
compoplot               Genotype composition plot
coords.monmonier        Returns original points in results paths of an
                        object of class 'monmonier'
dapc                    Discriminant Analysis of Principal Components
                        (DAPC)
dapcIllus               Simulated data illustrating the DAPC
df2genind               Convert a data.frame of allele data to a genind
                        object.
dist.genpop             Genetic distances between populations
eHGDP                   Extended HGDP-CEPH dataset
export_to_mvmapper      Export analysis for mvmapper visualisation
extract.PLINKmap        Reading PLINK Single Nucleotide Polymorphism
                        data
fasta2DNAbin            Read large DNA alignments into R
fasta2genlight          Extract Single Nucleotide Polymorphism (SNPs)
                        from alignments
find.clusters           find.cluster: cluster identification using
                        successive K-means
findMutations           Identify mutations between DNA sequences
gengraph                Genetic transitive graphs
genind-class            adegenet formal class (S4) for individual
                        genotypes
genind2df               Convert a genind object to a data.frame.
genind2genpop           Conversion from a genind to a genpop object
genlight-class          Formal class "genlight"
genpop-class            adegenet formal class (S4) for allele counts in
                        populations
glPca                   Principal Component Analysis for genlight
                        objects
glPlot                  Plotting genlight objects
glSim                   Simulation of simple genlight objects
glSum                   Auxiliary functions for genlight objects
global.rtest            Global and local tests
haploGen                Simulation of genealogies of haplotypes
hier                    Access and manipulate the population hierarchy
                        for genind or genlight objects.
hybridize               Function hybridize takes two genind in inputs
                        and generates hybrids individuals having one
                        parent in both objects.
hybridtoy               Toy hybrid dataset
import2genind           Importing data from several softwares to a
                        genind object
inbreeding              Likelihood-based estimation of inbreeding
indInfo-class           Virtual classes for adegenet
initialize,genind-method
                        genind constructor
initialize,genpop-method
                        genpop constructor
isPoly-methods          Assess polymorphism in genind/genpop objects
loadingplot             Represents a cloud of points with colors
makefreq                Compute allelic frequencies
microbov                Microsatellites genotypes of 15 cattle breeds
minorAllele             Compute minor allele frequency
monmonier               Boundary detection using Monmonier algorithm
nancycats               Microsatellites genotypes of 237 cats from 17
                        colonies of Nancy (France)
old2new_genind          Convert objects with obsolete classes into new
                        objects
pairDistPlot            Pairwise distance plots
propShared              Compute proportion of shared alleles
propTyped-methods       Compute the proportion of typed elements
read.fstat              Reading data from Fstat
read.genepop            Reading data from Genepop
read.genetix            Reading data from GENETIX
read.snp                Reading Single Nucleotide Polymorphism data
read.structure          Reading data from STRUCTURE
repool                  Pool several genotypes into a single dataset
rupica                  Microsatellites genotypes of 335 chamois
                        (Rupicapra rupicapra) from the Bauges mountains
                        (France)
scaleGen                Compute scaled allele frequencies
scatter.dapc            Graphics for Discriminant Analysis of Principal
                        Components (DAPC)
selPopSize              Select genotypes of well-represented
                        populations
seploc                  Separate data per locus
seppop                  Separate genotypes per population
seqTrack                SeqTrack algorithm for reconstructing
                        genealogies
setPop                  Manipulate the population factor of genind
                        objects.
showmekittens           When you need a break...
sim2pop                 Simulated genotypes of two georeferenced
                        populations
snapclust               Maximum-likelihood genetic clustering using EM
                        algorithm
snapclust.choose.k      Choose the number of clusters for snapclust
                        using AIC, BIC or AICc
snpposi.plot            Analyse the position of polymorphic sites
snpzip                  Identification of structural SNPs
spca                    Spatial principal component analysis
spcaIllus               Simulated data illustrating the sPCA
spca_randtest           Monte Carlo test for sPCA
strata                  Access and manipulate the population strata for
                        genind or genlight objects.
swallowtails            Microsatellites genotypes of 781 swallowtail
                        butterflies from 40 populations in Alberta and
                        British Columbia, Canada
tab                     Access allele counts or frequencies
truenames               Restore true labels of an object
xvalDapc                Cross-validation for Discriminant Analysis of
                        Principal Components (DAPC)
