gl2snapp

-- name of the genlight object containing the SNP data [required]

-- file name of the output file (including extension)[default snapp.nex]

outfile

-- 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.

outpath

-- 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]

verbose

The output nexus file contains the snp data and relevant PAUP command lines suitable for BEAUti.

Functions are provided that facilitate the import and analysis of
SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. The main focus is on data generated
by DarT (Diversity Arrays Technology). However, once SNP or related fragment
presence/absence data from any source is imported into a genlight object many
of the functions can be used. Functions are available for input and output of
SNP and silicodart data, for reporting on and filtering on various criteria
(e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency).
Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions
are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data
between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.

Bernd Gruber

gl2snapp: Convert a genlight object to nexus format suitable for phylogenetic analysis by SNAPP (via BEAUti)

Description

Usage

Arguments

References

Examples