gl2snapp: Converts a genlight object to nexus format suitable for...
In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis
gl2snapp R Documentation
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)
green-striped-gecko/dartR documentation built on Jan. 31, 2024, 10:14 a.m.
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| gl2snapp | R Documentation |
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)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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