align.clustal           CLUSTAL Alignment
align.folder            Align Sequences in a Folder
align.mafft             MAFFT Alignment
allele.freq.format      Compiles and Formats Allele Frequencies
allele.freqs            Allele Frequencies
allele.split            Split Alleles For Diploid Data
allelic.richness        Allelic Richness
as.data.frame.gtypes    Coerce to a Data Frame
as.dna.seq              Format List of DNA Sequences
as.matrix.gtypes        Coerce to a Matrix
base.freqs              Base Frequencies
bowhead.snp.position    Bowhead Whale SNP Genotype Groups
bowhead.snps            Bowhead Whale SNP Genotypes
check.genotypes         Run All Genotype QA/QC Tests
check.gtypes            Create a gtypes object
check.seqs              Run All Sequence QA/QC Tests
clumpp.run              Run CLUMPP
create.consensus        Consensus Sequence
decode                  Decode 'gtypes'
diversity               Unbiased Estimate of Diversity
dolph.haps              Dolphin mtDNA Haplotype Sequences
dolph.msats             Dolphin Microsatellite Genotypes
dolph.seqs              Dolphin mtDNA Sequences
dolph.strata            Dolphin Genetic Stratification and Haplotypes
dup.genotypes           Duplicate Genotypes
exptd.het               Expected Heterozygosity
fastsimcoal.run         Run FASTSIMCOAL
fisher.method.p         Fisher's Method p-value
fixed.differences       Fixed Differences
fixed.sites             Fixed Sites
fst.to.nm               Nm from Fst
gelato.plot             Plot GELATo
gelato.run              GELATo - Group ExcLusion and Assignment Test
gen.data.from.freq      Convert Haplotype Frequency Matrices
genepop.run             Run GENEPOP
gtype.struct.func       Population Structure Statistic Functions
h.stats                 Estimate Fixation Indices
hap.freqs               Haplotype Frequencies
haplotype.likelihoods   Haplotype Likelihoods
haplotypic.diversity    Haplotypic Diversity
hwe.genepop             Hardy-Weinberg Equilibrium
is.diploid              Check Ploidy
is.gtype.struct.func    Check Population Structure Function
is.ti.tv                Transition / Transversion Ratio
iupac.code              IUPAC Code
jack.hwe                Hardy-Weinberg Equlibrium Jackknife
jmodeltest.run          jModelTest
label.haplotypes        Find and label haplotypes
linkage.genepop         Linkage Disequlibrium
locus.cols              Locus Information
low.freq.subs           Low Frequency Substitutions
merge.gtypes            Merge gtypes
most.distant.sequences
                        Most Distant Sequences
na.omit.gtypes          Omit Missing Data
nei.Da                  Nei's Da
nucleotide.divergence   Nucleotide Divergence
nucleotide.diversity    Nucleotide Diversity
num.alleles             Number of Alleles
num.alleles.shared      Number of Shared Alleles
num.gens.eq             Number of Generations to Equilibrium
num.missing             Number Missing Data
obsvd.het               Observed Heterozygosity
overall.test            Population Differentiation Tests
p.val                   Permutation Test P-value
pairwise.shared.loci    Calculate Pairwise Shared Loci
pct.unique.haplotypes   Percent Unique Haplotypes
phase.filter            PHASE
print.gtypeSummary      Print gtypeSummary
read.arlequin           Read and Write Arlequin Files
read.fasta              Read and Write FASTA
read.gen.data           Read Genetic Data
read.mega               Read and Write MEGA
relabel.sequences       Relabel Sequences
restratify              Restratify gtypes
sequence.summary        Sequence Summary
shared.haps             Shared Haplotypes
sim.gamma.haps          Simulates Haplotypes
smry.by.locus           By-Locus Summaries
smry.by.sample          By-Sample Summaries
stat.chi2               CHI-squared Analysis of Population Structure
stat.d.jost             Jost's D Estimate of Population Divergence
stat.fst                Fst Analysis of Population Structure
stat.fst.prime          F'st analysis of population structure
stat.gst                Gst Analysis of Population Structure
stat.gst.dbl.prime      G"st Analysis of Population Structure
stat.gst.prime.hedrick
                        Hedrick's G'st Analysis of Population Structure
stat.gst.prime.nei      Nei's G'st Analysis of Population Structure
stat.phist              PHIst Analysis of Population Structure
stopifnot.gtype.struct.func
                        Check gtype Population Structure Function
strata.pairs            Strata Pairs
strata.split            Split Strata
strataG-package         Summaries and population structure analyses of
                        haplotypic and genotypic data
structure.evanno        Run Evanno Method on STRUCTURE Results
structure.parse.q.mat   Parse Q-Matrix Text
structure.plot          Plot STRUCTURE Results
structure.read          STRUCTURE
subset.gtypes           Subset a gtypes Object
summarize.loci          Locus Summaries
summarize.sequences     DNA Sequence Summaries
summary.gtypes          Summarize gtypes Object
tajimas.d               Tajima's D
theta                   Theta
trim.ns                 Trim N's From Sequences
valid.iupac.codes       Valid IUPAC Codes
variable.sites          Variable Sites
wright.fst              Wright's Fst
write.gtypes            write.gtypes
write.snapp.nexus       Write NEXUS File for SNAPP
