| gl2phylip {dartR.base} | R Documentation |
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)
See Also
Other linker:
gl2bayesAss(),
gl2bayescan(),
gl2bpp(),
gl2demerelate(),
gl2eigenstrat(),
gl2faststructure(),
gl2gds(),
gl2genalex(),
gl2genepop(),
gl2geno(),
gl2gi(),
gl2hiphop(),
gl2plink(),
gl2related(),
gl2sa(),
gl2structure(),
gl2treemix(),
gl2vcf()
Examples
result <- gl2phylip(testset.gl, outfile='test.txt', bstrap=10)