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pegas (version 0.8-2)

Population and Evolutionary Genetics Analysis System

Description

Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences and micro-satellites including coalescence analyses.

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Version

Install

install.packages('pegas')

Monthly Downloads

9,493

Version

0.8-2

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

September 25th, 2015

Functions in pegas (0.8-2)

Edit Allelic Data with R's Data Editor

Minimum Spanning Tree

Ramos-Onsins--Rozas Test of Neutrality

Conversion Among Allelic Data Classes

Population Parameter THETA using Expected Number of Alleles

Haplotype Frequencies With a Covariate

Population and Evolutionary Genetics Analysis System

Linkage Disequilibrium

Information From VCF Files

Utily Functions for pegas

Read Genetix Data Files

Heterozygosity at a Locus Using Gene Frequencies

Comparison Between Two Haplotypes

Bind Loci Objects

Read Variant Calling Format Files

Nucleotide Diversity

Population Parameter THETA using Segregating Sites

Edit the Layout of a Haplotype Network

Read Allelic Data Files

subset.haplotype

Subsetting and Filtering Haplotypes

Test of Hardy--Weinberg Equilibrium

Jaguar Micro-Satellites

Population Parameter THETA Using Genealogy

Haplotype Networks

Build Loci Object From Matrix of Alleles

Haplotype Extraction and Frequencies

Print and Summaries of Loci Objects

Test of the Neutral Mutation Hypothesis

Haplotype Extraction and Frequencies From Allelic Data

Tajima Relative Rate Test of Molecular Clock

Mismatch Distribution

Geodesic Distances

Analysis of Molecular Variance

Population Parameter THETA From Micro-Satellites

Write Allelic Data Files

Site Frequency Spectrum

Manipulate Geographic Coordinates

Population Parameter THETA using Homozygosity