dartR: gl2phylip – R documentation

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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

Author(s)

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

Examples

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

dartR

Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis

v1.9.6

GPL-2

Authors

Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb]

Initial release

2021-04-29