gl2snapp: Converts a genlight object to nexus format suitable for...

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Converts a genlight object to nexus format suitable for phylogenetic analysis by SNAPP (via BEAUti)

Description

The output nexus file contains the SNP data and relevant PAUP command lines suitable for BEAUti.

Usage

gl2snapp(x, outfile = "snapp.nex", outpath = tempdir(), verbose = NULL)

Arguments

x	Name of the genlight object containing the SNP data [required].
outfile	File name of the output file (including extension) [default "snapp.nex"].
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.
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

returns no value (i.e. NULL)

Author(s)

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

References

Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N.A. and RoyChoudhury, A. (2012). Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution 29:1917-1932.

Examples

gl2snapp(testset.gl)

dartR documentation built on June 8, 2023, 6:48 a.m.