Converts a genlight object to nexus format suitable for phylogenetic analysis by SNAPP (via BEAUti)
Source:R/gl2snapp.r
gl2snapp.Rd
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)