gl.tree.nj

This function is a wrapper for the nj function or package ape applied to Euclidean
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, data from other sequencing platforms can be used once 'SNP' or related
fragment presence/absence data from any source is imported. Genetic datasets
are stored in a derived 'genlight' format (package 'adegenet'), that allows for
a very compact storage of data and metadata. Functions are available for
importing and exporting of 'SNP' and 'silicodart' data, for reporting on and
filtering on various criteria (e.g. 'CallRate', heterozygosity, reproducibility,
maximum allele frequency). Additional functions are available for visualization
(e.g. Principle Coordinate Analysis) and creating a spatial representation
using maps. 'dartR' supports also the analysis of 3rd party software package
such as 'newhybrid', 'structure', 'NeEstimator' and 'blast'. Since version
2.0.3 we also implemented simulation functions, that allow to forward simulate
'SNP' dynamics under different population and evolutionary dynamics.
Comprehensive tutorials and support can be found at our 'github' repository:
github.com/green-striped-gecko/dartR/. If you want to cite 'dartR', you find
the information by typing citation('dartR') in the console.

Bernd Gruber

dartR

Importing and Analysing 'SNP' and 'Silicodart' Data Generated by
Genome-Wide Restriction Fragment Analysis

Arthur Georges

Jose L. Mijangos

Carlo Pacioni

Diana Robledo-Ruiz

Peter J. Unmack

Oliver Berry

Lindsay V. Clark

Floriaan Devloo-Delva

Eric Archer

gl.tree.nj function

<dl><dt>x</dt>
<dd>Name of the genlight object containing the SNP data [required].</dd>
<dt>d_mat</dt>
<dd>Distance matrix [default NULL].</dd>
<dt>type</dt>
<dd>Type of dendrogram "phylogram"|"cladogram"|"fan"|"unrooted"
[default "phylogram"].</dd>
<dt>outgroup</dt>
<dd>Vector containing the population names that are the outgroups
[default NULL].</dd>
<dt>labelsize</dt>
<dd>Size of the labels as a proportion of the graphics default
[default 0.7].</dd>
<dt>treefile</dt>
<dd>Name of the file for the tree topology using Newick format 
[default NULL].</dd>
<dt>verbose</dt>
<dd>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].</dd></dl>

Arguments

Custodian: Arthur Georges (Post to
<a href="https://groups.google.com/d/forum/dartr">https://groups.google.com/d/forum/dartr</a>)

Author

Outputs an nj tree to summarize genetic similarity among populations — gl.tree.nj

<dl>

<dt>x</dt>
<dd>Name of the genlight object containing the SNP data [required].</dd>


<dt>d_mat</dt>
<dd>Distance matrix [default NULL].</dd>


<dt>type</dt>
<dd>Type of dendrogram "phylogram"|"cladogram"|"fan"|"unrooted"
[default "phylogram"].</dd>


<dt>outgroup</dt>
<dd>Vector containing the population names that are the outgroups
[default NULL].</dd>


<dt>labelsize</dt>
<dd>Size of the labels as a proportion of the graphics default
[default 0.7].</dd>


<dt>treefile</dt>
<dd>Name of the file for the tree topology using Newick format 
[default NULL].</dd>


<dt>verbose</dt>
<dd>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].</dd>

</dl>

Custodian: Arthur Georges (Post to
<a href='https://groups.google.com/d/forum/dartr'>https://groups.google.com/d/forum/dartr</a>)

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

Description

Usage

Value

Arguments

Author

Details

Examples