gl2phylip: Creates a Phylip input distance matrix from a genlight (SNP)...

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Creates a Phylip input distance matrix from a genlight (SNP) {adegenet} object

Description

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

Usage

gl2phylip(
  x,
  outfile = "phyinput.txt",
  outpath = tempdir(),
  bstrap = 1,
  verbose = NULL
)

Arguments

x	Name of the genlight object containing the SNP or presence/absence (SilicoDArT) data [required].
outfile	Name of the file to become the input file for phylip [default "phyinput.txt"].
outpath	Path where to save the output file [default tempdir(), mandated by CRAN]. Use outpath=getwd() or outpath='.' when calling this function to direct output files to your working directory.
bstrap	Number of bootstrap replicates [default 1].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]

Value

Matrix of Euclidean distances between populations.

Author(s)

Custodian: Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

Examples

result <- gl2phylip(testset.gl, outfile='test.txt', bstrap=10)

green-striped-gecko/dartR documentation built on Jan. 31, 2024, 10:14 a.m.