Learn R Programming

pegas (version 1.4)

Population and Evolutionary Genetics Analysis System

Description

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.

Copy Link

Version

Install

install.packages('pegas')

Monthly Downloads

9,017

Version

1.4

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

December 8th, 2025

Functions in pegas (1.4)

dist.asd

Allelic Sharing Distance
geoTrans

Manipulate Geographical Coordinates
cophenetic.haploNet

Cophenetic Matrix on Haplotype Networks
dist.hamming

Hamming Distance
diffHaplo

Comparison Between Two Haplotypes
jaguar

Jaguar Micro-Satellites
haplotype

Haplotype Extraction and Frequencies
mjn

Median-Joining Network
haplotype.loci

Haplotype Extraction and Frequencies From Allelic Data
read.gtx

Read Genetix Data Files
plotNetMDS

Plot Networks With MDS Layout
read.vcf

Read Variant Calling Format Files
read.loci

Read Allelic Data Files
nuc.div

Nucleotide Diversity
haploNet

Haplotype Networks
site.spectrum

Site Frequency Spectrum
as.loci

Conversion Among Allelic Data Classes
hap.div

Haplotype Diversity
na.omit.loci

Missing Allelic Data
mst

Minimum Spanning Tree and Network
theta.h

Population Parameter THETA using Homozygosity
rr.test

Tajima Relative Rate Test of Molecular Clock
geod

Geodesic Distances
haploFreq

Haplotype Frequencies With a Covariate
mutations

Plot Mutations on Networks
sw

Sliding Windows
theta.k

Population Parameter THETA using Expected Number of Alleles
heterozygosity

Heterozygosity at a Locus Using Gene Frequencies
tajima.test

Test of the Neutral Mutation Hypothesis
write.loci

Write Allelic Data Files
replot

Edit the Layout of a Haplotype Network
subset.haplotype

Subsetting and Filtering Haplotypes
hw.test

Test of Hardy--Weinberg Equilibrium
pegas-package

Population and Evolutionary Genetics Analysis System
getHaploNetOptions

Options to Plot haploNet Objects
stairway

The Stairway Plot
theta.tree

Population Parameter THETA Using Genealogy
utilities

Utily Functions for pegas
theta.msat

Population Parameter THETA From Micro-Satellites
theta.s

Population Parameter THETA using Segregating Sites
summary.loci

Print and Summaries of Loci Objects
MMD

Mismatch Distribution
LD

Linkage Disequilibrium
bind.loci

Bind Loci Objects
F4

F-Statistics From Patterson et al
amova

Analysis of Molecular Variance
alleles2loci

Build Loci Object From Matrix of Alleles
R2.test

Ramos-Onsins--Rozas Test of Neutrality
Fst

F-Statistics
LDscan

Multi-Locus Linkage Disequilibrium
edit.loci

Edit Allelic Data with R's Data Editor
all.equal.haploNet

Compare Two Haplotype Networks
by.loci

Summary by Population or Other Factor
VCFloci

Information From VCF Files
allelicrichness

Allelic Richness and Rarefaction Plots