F4                      F-Statistics From Patterson et al
Fst                     F-Statistics
LD                      Linkage Disequilibrium
LDscan                  Multi-Locus Linkage Disequilibrium
MMD                     Mismatch Distribution
R2.test                 Ramos-Onsins-Rozas Test of Neutrality
VCFloci                 Information From VCF Files
all.equal.haploNet      Compare Two Haplotype Networks
alleles2loci            Build Loci Object From Matrix of Alleles
allelicrichness         Allelic Richness and Rarefaction Plots
amova                   Analysis of Molecular Variance
as.loci                 Conversion Among Allelic Data Classes
bind.loci               Bind Loci Objects
by.loci                 Summary by Population of Other Factor
diffHaplo               Comparison Between Two Haplotypes
dist.asd                Allelic Sharing Distance
dist.hamming            Hamming Distance
edit.loci               Edit Allelic Data with R's Data Editor
geoTrans                Manipulate Geographical Coordinates
geod                    Geodesic Distances
getPloidy               Utily Functions for pegas
hap.div                 Haplotype Diversity
haploFreq               Haplotype Frequencies With a Covariate
haploNet                Haplotype Networks
haplotype               Haplotype Extraction and Frequencies
haplotype.loci          Haplotype Extraction and Frequencies From
                        Allelic Data
heterozygosity          Heterozygosity at a Locus Using Gene
                        Frequencies
hw.test                 Test of Hardy-Weinberg Equilibrium
jaguar                  Jaguar Micro-Satellites
mjn                     Median-Joining Network
mst                     Minimum Spanning Tree and Network
na.omit.loci            Missing Allelic Data
nuc.div                 Nucleotide Diversity
pegas-package           Population and Evolutionary Genetics Analysis
                        System
plotNetMDS              Plot Networks With MDS Layout
read.gtx                Read Genetix Data Files
read.loci               Read Allelic Data Files
read.vcf                Read Variant Calling Format Files
replot                  Edit the Layout of a Haplotype Network
rr.test                 Tajima Relative Rate Test of Molecular Clock
site.spectrum           Site Frequency Spectrum
stairway                The Stairway Plot
subset.haplotype        Subsetting and Filtering Haplotypes
summary.loci            Print and Summaries of Loci Objects
sw                      Sliding Windows
tajima.test             Test of the Neutral Mutation Hypothesis
theta.h                 Population Parameter THETA using Homozygosity
theta.k                 Population Parameter THETA using Expected
                        Number of Alleles
theta.msat              Population Parameter THETA From
                        Micro-Satellites
theta.s                 Population Parameter THETA using Segregating
                        Sites
theta.tree              Population Parameter THETA Using Genealogy
write.loci              Write Allelic Data Files
