gl.tree.nj

-- Name of the genlight object containing the SNP data or a genind object containing presence absence data [required]

-- Type of dendrogram phylogram|cladogram|fan|unrooted [Default Phylogram]

type

-- Vector containing the population names that are the outgroups [Default NULL]

outgroup

-- Size of the labels as a proportion of the graphics default [Default 0.7]

labelsize

This function is a wrapper for the nj{ape} function applied to Euclidian
distances calculated from the genlight object.

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.

gl.tree.nj: Output an nj tree to summarize genetic similarity among populations

Description

Usage

Arguments

Value

Examples