dartR (version 1.1.11)

gl2svdquartets: Convert a genlight object to nexus format PAUP SVDquartets

Description

The output nexus file contains the snp data in one of two forms, depending upon what you regard as most appropriate. One form, that used by Chifman and Kubatko, has two lines per individual, one providing the reference SNP the second providing the alternate SNP (method=1). A second form, recommended by Dave Swofford, has a single line per individual, resolving heterozygous SNPs by replacing them with standard ambiguity codes (method=2).

Usage

gl2svdquartets(x, outfile = "svd.nex", outpath = tempdir(),
  method = 2, v = 2)

Arguments

x

-- name of the genlight object containing the SNP data [required]

outfile

-- file name of the output file (including extension).

outpath

-- path where to save the output file (set to tempdir by default)

method

-- method = 1, nexus file with two lines per individual; method = 2, nexus file with one line per individual, ambiguity codes [default 2]

v

-- verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2]

Details

Reference: Chifman, J. and L. Kubatko. 2014. Quartet inference from SNP data under the coalescent, Bioinformatics, 30: 3317-3324

Examples

# NOT RUN {
gl2svdquartets(testset.gl[1:20,1:100])
# }