adegenet

Compute Akaike Information Criterion (AIC) for snapclust

Compute Akaike Information Criterion for small samples (AICc) for snapclust

Compute Bayesian Information Criterion (BIC) for snapclust

Seasonal influenza (H3N2) HA segment data

Hardy-Weinberg Equilibrium test for multilocus data

Expected heterozygosity (Hs)

Test differences in expected heterozygosity (Hs)

Compute Akaike Information Criterion for small samples (AICc) for snapclust

Formal class "SNPbin"

Accessors for adegenet objects

The adegenet package

Converting genind/genpop objects to other classes

Conversion to class "SNPbin"

Conversion to class "genlight"

Compute and optimize a-score for Discriminant Analysis of Principal Components (DAPC)

Auxiliary functions for adegenet

Function to choose a connection network

Represents a cloud of points with colors

Genotype composition plot

Returns original points in results paths of an object of class 'monmonier'

Discriminant Analysis of Principal Components (DAPC)

Graphics for Discriminant Analysis of Principal Components (DAPC)

Simulated data illustrating the DAPC

Convert a data.frame of allele data to a genind object.

Genetic distances between populations

Internal C routines

Extended HGDP-CEPH dataset

Export analysis for mvmapper visualisation

Read large DNA alignments into R

Extract Single Nucleotide Polymorphism (SNPs) from alignments

find.cluster: cluster identification using successive K-means

Genetic transitive graphs

adegenet formal class (S4) for individual genotypes

Convert a genind object to a data.frame.

Conversion from a genind to a genpop object

Formal class "genlight"

adegenet formal class (S4) for allele counts in populations

Auxiliary functions for genlight objects

Principal Component Analysis for genlight objects

Plotting genlight objects

Simulation of simple genlight objects

Simulation of genealogies of haplotypes

Access and manipulate the population hierarchy for genind or genlight objects.

Function hybridize takes two genind in inputs and generates hybrids individuals having one parent in both objects.

Toy hybrid dataset

Importing data from several softwares to a genind object

Likelihood-based estimation of inbreeding

Assess polymorphism in genind/genpop objects

Represents a cloud of points with colors

Compute allelic frequencies

Microsatellites genotypes of 15 cattle breeds

Compute minor allele frequency

Boundary detection using Monmonier algorithm

Identify mutations between DNA sequences

Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France)

genind constructor

genpop constructor

Convert objects with obsolete classes into new objects

Pairwise distance plots

Manipulate the population factor of genind objects.

Compute proportion of shared alleles

Compute the proportion of typed elements

Reading PLINK Single Nucleotide Polymorphism data

Reading data from Fstat

Reading data from Genepop

Reading data from GENETIX

Reading Single Nucleotide Polymorphism data

Reading data from STRUCTURE

Pool several genotypes into a single dataset

Microsatellites genotypes of 335 chamois (Rupicapra rupicapra) from the Bauges mountains (France)

Compute scaled allele frequencies

Select genotypes of well-represented populations

Separate data per locus

Separate genotypes per population

SeqTrack algorithm for reconstructing genealogies

Importing data from an alignement of sequences to a genind object

Web servers for adegenet

When you need a break...

Simulated genotypes of two georeferenced populations

Maximum-likelihood genetic clustering using EM algorithm

Choose the number of clusters for snapclust using BIC

Analyse the position of polymorphic sites

Identification of structural SNPs

Spatial principal component analysis

Global and local tests

Simulated data illustrating the sPCA

Monte Carlo test for sPCA

Access and manipulate the population strata for genind or genlight objects.

Microsatellites genotypes of 781 swallowtail butterflies from 40 populations in Alberta and British Columbia, Canada

Access allele counts or frequencies

Restore true labels of an object

Virtual classes for adegenet

Functions to access online resources for adegenet

Cross-validation for Discriminant Analysis of Principal Components (DAPC)