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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)

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/RtmpWgoHDI/snapp.nex 
#> Completed: gl2snapp 
#> 
#> NULL