PairwiseDistances

Distances between each pair of trees

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) <doi:10.1016/j.mbs.2012.10.005>;
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

PairwiseDistances function

<dl><dt>trees</dt>
<dd>List of trees of class <code>phylo</code>.</dd>
<dt>Func</dt>
<dd>Function returning a distance between two trees.</dd>
<dt>valueLength</dt>
<dd>Integer specifying expected length of the value returned
by <code>Func</code>.</dd>
<dt>...</dt>
<dd>Additional arguments to <code>Func</code>.</dd></dl>

Arguments

Martin R. Smith (<a href="/link/martin.smith%40durham.ac.uk?package=TreeTools&version=1.9.0" data-mini-rdoc="TreeTools::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

Distances between each pair of trees — PairwiseDistances

<dl>

<dt>trees</dt>
<dd>List of trees of class <code>phylo</code>.</dd>


<dt>Func</dt>
<dd>Function returning a distance between two trees.</dd>


<dt>valueLength</dt>
<dd>Integer specifying expected length of the value returned
by <code>Func</code>.</dd>


<dt>...</dt>
<dd>Additional arguments to <code>Func</code>.</dd>

</dl>

Martin R. Smith (<a href='mailto:martin.smith@durham.ac.uk'>martin.smith@durham.ac.uk</a>)

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PairwiseDistances: Distances between each pair of trees

Description

Usage

Value

Arguments

Author

Examples