dartR (version 1.9.9.1)

gl2phylip: Create 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 data or a genind object containing presence absence 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

Examples

# NOT RUN {
result <- gl2phylip(testset.gl, outfile="test.txt", bstrap=10)
# }