Population and Evolutionary Genetics Analysis System
Compare Two Haplotype Networks
Build Loci Object From Matrix of Alleles
Allelic Richness and Rarefaction Plots
Analysis of Molecular Variance
Bind Loci Objects
Summary by Population or Other Factor
Conversion Among Allelic Data Classes
Cophenetic Matrix on Haplotype Networks
Comparison Between Two Haplotypes
Allelic Sharing Distance
Hamming Distance
Edit Allelic Data with R's Data Editor
F-Statistics From Patterson et al
F-Statistics
Geodesic Distances
Manipulate Geographical Coordinates
Haplotype Diversity
Haplotype Frequencies With a Covariate
Haplotype Networks
Haplotype Extraction and Frequencies From Allelic Data
Haplotype Extraction and Frequencies
Heterozygosity at a Locus Using Gene Frequencies
Test of Hardy--Weinberg Equilibrium
Linkage Disequilibrium
Multi-Locus Linkage Disequilibrium
Median-Joining Network
Mismatch Distribution
Minimum Spanning Tree and Network
Plot Mutations on Networks
Missing Allelic Data
Nucleotide Diversity
Options to Plot haploNet Objects
Population and Evolutionary Genetics Analysis System
Plot Networks With MDS Layout
Ramos-Onsins--Rozas Test of Neutrality
Read Genetix Data Files
Read Allelic Data Files
Read Variant Calling Format Files
Edit the Layout of a Haplotype Network
Tajima Relative Rate Test of Molecular Clock
Site Frequency Spectrum
The Stairway Plot
Subsetting and Filtering Haplotypes
Print and Summaries of Loci Objects
Sliding Windows
Test of the Neutral Mutation Hypothesis
Population Parameter THETA using Homozygosity
Population Parameter THETA using Expected Number of Alleles
Population Parameter THETA From Micro-Satellites
Population Parameter THETA using Segregating Sites
Population Parameter THETA Using Genealogy
Utily Functions for pegas
Information From VCF Files
Write Allelic Data Files
Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.