RootTree

RootOnNode

UnrootTree

<code>RootTree()</code> roots a tree on the smallest clade containing the specified
tips;
<code>RootOnNode()</code> roots a tree on a specified internal node;
<code>UnrootTree()</code> collapses a root node, without the undefined behaviour
encountered when using <code>ape::unroot()</code> on trees in
preorder.

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

RootTree function

<dl><dt>tree</dt>
<dd>A tree of class <code>phylo</code>, or a list of trees
of class <code>list</code> or <code>multiPhylo</code>.</dd>
<dt>outgroupTips</dt>
<dd>Vector of type character, integer or logical, specifying
the names or indices of the tips to include in the outgroup.
If <code>outgroupTips</code> is a of type character, and a tree contains multiple tips
with a matching label, the first will be used.</dd>
<dt>node</dt>
<dd>integer specifying node (internal or tip) to set as the root.</dd>
<dt>resolveRoot</dt>
<dd>logical specifying whether to resolve the root node.</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

Root or unroot a phylogenetic tree — RootTree

<dl>

<dt>tree</dt>
<dd>A tree of class <code>phylo</code>, or a list of trees
of class <code>list</code> or <code>multiPhylo</code>.</dd>


<dt>outgroupTips</dt>
<dd>Vector of type character, integer or logical, specifying
the names or indices of the tips to include in the outgroup.
If <code>outgroupTips</code> is a of type character, and a tree contains multiple tips
with a matching label, the first will be used.</dd>


<dt>node</dt>
<dd>integer specifying node (internal or tip) to set as the root.</dd>


<dt>resolveRoot</dt>
<dd>logical specifying whether to resolve the root node.</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>)

RootTree: Root or unroot a phylogenetic tree

Description

Usage

Value

Arguments

Author

See Also

Examples