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

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

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

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

Examples

# \donttest{
result <- gl2phylip(testset.gl, outfile='test.txt', bstrap=10)
#> Starting gl2phylip 
#>   Processing genlight object with SNP data
#>   Warning: genlight object contains monomorphic loci
#> Converting to a matrix of frequencies, locus by populations
#> Computing Euclidean distances
#> Writing the Phylip input file /tmp/RtmpaU40iz/test.txt 
#> Repeating calculations for 10 iterations
#> Closing output file test.txt 
#> Completed: gl2phylip 
#> 
# }