gl2phylip

Name of the genlight object containing the SNP data or a genind object containing presence absence data [required]

Name of the file to become the input file for phylip [default phyinput.txt]

outfile

path where to save the output file (set to tempdir by default)

outpath

Number of bootstrap replicates [default 1]

bstrap

This function calculates and returns a matrix of Euclidean distances between populations
and produces an input file for the phylogenetic program Phylip (Joe Felsenstein).

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.

gl2phylip: Create a Phylip input distance matrix from a genlight (SNP) or genind (SilicoDarT) {adegenet} object

Description

Usage

Arguments

Value

Examples