NJTree

<code>NJTree()</code> generates a rooted neighbour joining tree from a phylogenetic
dataset.

Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.

Martin R. Smith

TreeTools

Create, Modify and Analyse Phylogenetic Trees

Emmanuel Paradis

Robert Noble

NJTree function

<dl><dt>dataset</dt>
<dd>A phylogenetic data matrix of phangorn class <code>phyDat</code>,
whose names correspond to the labels of any accompanying tree.</dd>
<dt>edgeLengths</dt>
<dd>Logical specifying whether to include edge lengths.</dd>
<dt>ambig, ratio</dt>
<dd>Settings of <code>ambig</code> and <code>ratio</code> to be used when
computing <code>Hamming()</code> distances between sequences.</dd></dl>

Arguments

<a href="https://orcid.org/0000-0001-5660-1727">Martin R. Smith</a>
(<a href="/link/martin.smith%40durham.ac.uk?package=TreeTools&version=1.12.0" data-mini-rdoc="TreeTools::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

Generate a neighbour joining tree — NJTree

<dl>

<dt>dataset</dt>
<dd>A phylogenetic data matrix of phangorn class <code>phyDat</code>,
whose names correspond to the labels of any accompanying tree.</dd>


<dt>edgeLengths</dt>
<dd>Logical specifying whether to include edge lengths.</dd>


<dt>ambig, ratio</dt>
<dd>Settings of <code>ambig</code> and <code>ratio</code> to be used when
computing <code>Hamming()</code> distances between sequences.</dd>

</dl>

<a href='https://orcid.org/0000-0001-5660-1727'>Martin R. Smith</a>
(<a href='mailto:martin.smith@durham.ac.uk'>martin.smith@durham.ac.uk</a>)

NJTree: Generate a neighbour joining tree

Description

Usage

Value

Arguments

Author

See Also

Examples