Output an nj tree to summarize genetic similarity among populations
This function is a wrapper for the nj{ape} function applied to Euclidian distances calculated from the genlight object.
gl.tree.nj( x, type = "phylogram", outgroup = NULL, labelsize = 0.7, treefile = NULL, verbose = NULL )
x |
– name of the genlight object containing the SNP data [required] |
type |
– Type of dendrogram phylogram|cladogram|fan|unrooted [Default Phylogram] |
outgroup |
– Vector containing the population names that are the outgroups [Default NULL] |
labelsize |
– Size of the labels as a proportion of the graphics default [Default 0.7] |
treefile |
– Name of the file for the tree topology using Newick format [Default NULL]. |
verbose |
– specify the level of verbosity: 0, silent, fatal errors only; 1, flag function begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2] |
A tree file of class phylo
Arthur Georges (Post to https://groups.google.com/d/forum/dartr)
# SNP data gl.tree.nj(testset.gl,type="fan") # Tag P/A data gl.tree.nj(testset.gs,type="fan")
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