gl.amova

-- name of the genlight containing the SNP genotypes, with population information [required]

-- number of permuations to perform for hypothesis testing [default 100]. Please note should be set to 1000 for analysis.]

nperm

This script performs an AMOVA based on the genetic distance matrix from stamppNeisD() [package StAMPP] using the amova() function from the package PEGAS for exploring within and between population variation. For detailed information use their help pages: ?pegas::amova, ?StAMPP::stamppAmova

Functions are provided that facilitate the import and analysis of
SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. The main focus is on data generated
by DarT (Diversity Arrays Technology). However, once SNP or related fragment
presence/absence data from any source is imported into a genlight object many
of the functions can be used. Functions are available for input and output of
SNP and silicodart data, for reporting on and filtering on various criteria
(e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency).
Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions
are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data
between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.

gl.amova: Performs and AMOVA using genlight data.

Description

Usage

Arguments

Value