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

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].

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.

Author

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

Examples

gl2snapp(testset.gl)
#> Starting gl2snapp 
#>   Processing genlight object with SNP data
#>   Extacting SNP data and creating records for each individual
#>   Writing results to nexus file /tmp/RtmpMqupE6/snapp.nex 
#> Completed: gl2snapp 
#> 
#> NULL