RenumberTips

RenumberTips.phylo

RenumberTips.multiPhylo

RenumberTips.list

RenumberTips.NULL

A tree of class <code><a rd-options="ape:read.tree" href="/link/phylo?package=TreeTools&version=1.6.0&to=ape%3Aread.tree" data-mini-rdoc="ape:read.tree::phylo">phylo</a></code>.

tree

A character vector containing the values of
<code>tree$tip.label</code> in the desired sort order, or an object
(perhaps of class <code>phylo</code> or <code>Splits</code>) with tip labels.

tipOrder

<code>RenumberTips(tree, tipOrder)</code> sorts the tips of a phylogenetic tree <code>tree</code>
such that the indices in <code>tree$edge[, 2]</code> correspond to the order of
leaves given in <code>tipOrder</code>.

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, 2021) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013) <doi:10.1016/j.mbs.2012.10.005>;
artificial extinction (Asher & Smith, 2021) <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 <http://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

RenumberTips function

A tree of class <code><a rd-options='ape:read.tree' href='phylo'>phylo</a></code>.

RenumberTips: Renumber a tree's tips

Description

Usage

Arguments

Value

See Also

Examples