| gl2snapp {dartR.base} | R Documentation |
Converts a genlight object to nexus format suitable for phylogenetic analysis by SNAPP (via BEAUti) @family linker
Description
The output nexus file contains the SNP data and relevant PAUP command lines suitable for BEAUti.
Usage
gl2snapp(x, outfile = "snapp.nex", outpath = NULL, 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 global working directory or if not specified, tempdir()]. |
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, outpath=tempdir())