Aeut                    Oomycete root rot pathogen *Aphanomyces
                        euteiches* AFLP data
Pinf                    Phytophthora infestans data from Mexico and
                        South America.
Pram                    Phytophthora ramorum data from OR Forests and
                        Nurseries (OR and CA)
aboot                   Calculate a dendrogram with bootstrap support
                        using any distance applicable to genind or
                        genclone objects.
as.snpclone             Create a snpclone object from a genlight
                        object.
bitwise.dist            Calculate dissimilarity or Euclidean distance
                        for genlight objects
boot.ia                 Bootstrap the index of association
bootgen2genind          Switch between genind and genclone objects.
bruvo.boot              Create a tree using Bruvo's Distance with
                        non-parametric bootstrapping.
bruvo.dist              Bruvo's distance for microsatellites
bruvo.msn               Create minimum spanning network of selected
                        populations using Bruvo's distance.
clonecorrect            Remove potential bias caused by cloned
                        genotypes in genind or genclone object.
cutoff_predictor        Predict cutoff thresholds for use with
                        mlg.filter
diss.dist               Calculate a distance matrix based on relative
                        dissimilarity
diversity_boot          Perform a bootstrap analysis on diversity
                        statistics
diversity_ci            Perform bootstrap statistics, calculate, and
                        plot confidence intervals.
diversity_stats         Produce a table of diversity statistics
filter_stats            Utilize all algorithms of mlg.filter
fix_replen              Find and fix inconsistent repeat lengths
genclone-class          GENclone and SNPclone classes
genind2genalex          Export data from genind objects to genalex
                        formatted *.csv files.
genotype_curve          Produce a genotype accumulation curve
getfile                 Get a file name and path and store them in a
                        list.
greycurve               Display a greyscale gradient adjusted to
                        specific parameters
ia                      Index of Association
imsn                    Create minimum spanning networks interactively
incomp                  Check for samples that are incomparable due to
                        missing data
info_table              Create a table summarizing missing data or
                        ploidy information of a genind or genclone
                        object
informloci              Remove all non-phylogentically informative loci
is.snpclone             Check for validity of a genclone or snpclone
                        object
locus_table             Create a table of summary statistics per locus.
make_haplotypes         Split samples from a genind object into
                        pseudo-haplotypes
missingno               Treat missing data
mlg                     Create counts, vectors, and matrices of
                        multilocus genotypes.
mlg.filter              MLG definitions based on genetic distance
mll                     Access and manipulate multilocus lineages.
mll.custom              Define custom multilocus lineages
mll.reset               Reset multilocus lineages
monpop                  Peach brown rot pathogen *Monilinia fructicola*
nei.dist                Calculate Genetic Distance for a genind or
                        genclone object.
old2new_genclone        Convert an old genclone object to a new
                        genclone object
partial_clone           Simulated data illustrating a Minimum Spanning
                        Network based on Bruvo's Distance
pgen                    Genotype Probability
plot_poppr_msn          Plot minimum spanning networks produced in
                        poppr.
poppr                   Produce a basic summary table for population
                        genetic analyses.
poppr-package           The 'poppr' R package
poppr.all               Process a list of files with poppr
poppr.amova             Perform Analysis of Molecular Variance (AMOVA)
                        on genind or genclone objects.
poppr.msn               Create a minimum spanning network of selected
                        populations using a distance matrix.
poppr_has_parallel      Determines whether openMP is support on this
                        system.
popsub                  Subset data by population
private_alleles         Tabulate alleles the occur in only one
                        population.
psex                    Probability of encountering a genotype more
                        than once by chance
rare_allele_correction
                        Correcting rare allele frequencies
read.genalex            Importing data from genalex formatted *.csv
                        files.
recode_polyploids       Recode polyploid microsatellite data for use in
                        frequency based statistics.
rraf                    Round Robin Allele Frequencies
rrmlg                   Round Robin Multilocus Genotypes
samp.ia                 Calculate random samples of the index of
                        association for genlight objects.
shufflepop              Shuffle individuals in a 'genclone' or 'genind'
                        object independently over each locus.
test_replen             Test repeat length consistency.
win.ia                  Calculate windows of the index of association
                        for genlight objects.
