Creates a Phylip input distance matrix from a genlight (SNP) {adegenet} object
Source:R/gl2phylip.r
gl2phylip.Rd
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]
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/RtmpWgoHDI/test.txt
#> Repeating calculations for 10 iterations
#> Closing output file test.txt
#> Completed: gl2phylip
#>
# }