LDgenepop               Linkage Disequlibrium
TiTvRatio               Transition / Transversion Ratio
alleleFreqs             Allele Frequencies
alleleSplit             Split Alleles For Diploid Data
allelicRichness         Allelic Richness
arlequin                Read and Write Arlequin Files
as.data.frame.gtypes    Convert 'gtypes' to data.frame or matrix
as.multidna             Convert to multidna
baseFreqs               Base Frequencies
bowhead.snp.position    Bowhead Whale SNP Genotype Groups
bowhead.snps            Bowhead Whale SNP Genotypes
clumpp                  Run CLUMPP
createConsensus         Consensus Sequence
df2gtypes               Convert a data.frame to gtypes
dloop.g                 Dolphin dLoop gtypes Object
dolph.haps              Dolphin mtDNA Haplotype Sequences
dolph.msats             Dolphin Microsatellite Genotypes
dolph.seqs              Dolphin mtDNA D-loop Sequences
dolph.strata            Dolphin Genetic Stratification and Haplotypes
dupGenotypes            Duplicate Genotypes
evanno                  Run Evanno Method on STRUCTURE Results
expandHaplotypes        Expand Haplotypes
fasta                   Read and Write FASTA
fixedDifferences        Fixed Differences
fixedSites              Fixed Sites
freq2GenData            Convert Haplotype Frequency Matrices
fsc.input               Input functions for fastsimcoal parameters
fscRead                 Read fastsimcoal output
fscRun                  Run fastsimcoal
fscWrite                Write fastsimcoal2 input files
fusFs                   Fu's Fs
gelato                  GELATo - Group ExcLusion and Assignment Test
genepop                 Run GENEPOP
gtypes-class            'gtypes' Class
gtypes.accessors        'gtypes' Accessors
gtypes2genind           Convert Between 'gtypes' And 'genind' objects.
gtypes2loci             Convert Between 'gtypes' And 'loci' objects.
gtypes2phyDat           Convert Between 'gtypes' And 'phyDat' objects.
heterozygosity          Heterozygosity
hweTest                 Hardy-Weinberg Equilibrium
initialize,gtypes-method
                        'gtypes' Constructor
is.gtypes               Test if object is 'gtypes'
iupac                   IUPAC Codes
labelHaplotypes         Find and label haplotypes
landscape2gtypes        Convert Rmetasim landscape
ldNe                    ldNe
lowFreqSubs             Low Frequency Substitutions
mRatio                  M ratio
maf                     Minor Allele Frequencies
mafft                   MAFFT Alignment
maverickRun             Run MavericK
mega                    Read and Write MEGA
mostDistantSequences    Most Distant Sequences
mostRepresentativeSequences
                        Representative Sequences
msats.g                 Dolphin Microsatellite gtypes Object
neiDa                   Nei's Da
nucleotideDivergence    Nucleotide Divergence
nucleotideDiversity     Nucleotide Diversity
numAlleles              Number of Alleles
numGenotyped            Number of Individuals Genotyped
numMissing              Number Missing Data
permuteStrata           Permute strata
phase                   PHASE
popGenEqns              Population Genetics Equations
popStructStat           Population structure statistics
popStructTest           Population Differentiation Tests
privateAlleles          Private Alleles
propUniqueAlleles       Proportion Unique Alleles
readGenData             Read Genetic Data
removeSequences         Remove Sequences
sequence2gtypes         Convert Sequences To 'gtypes'
sequenceLikelihoods     Sequence Likelihoods
sfs                     Site Frequency Spectrum
sharedLoci              Shared Loci
simGammaHaps            Simulate Haplotypes
strataG-package         Summaries and population structure analyses of
                        DNA sequence genotypic data
strataSplit             Split Strata
stratify                Stratify gtypes
structure               STRUCTURE
structurePlot           Plot STRUCTURE Results
summarizeAll            Summarize Genotypes and Sequences
summarizeInds           Individual Summaries
summarizeLoci           Locus Summaries
summarizeSeqs           Sequence Summaries
summary,gtypes-method   Summarize gtypes Object
tajimasD                Tajima's D
theta                   Theta
trimNs                  Trim N's From Sequences
variableSites           Variable Sites
write.nexus.snapp       Write NEXUS File for SNAPP
writeGtypes             Write 'gtypes'
