CalculateTreeDistance

Calls tree distance functions from trees or lists of trees

internal

Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for identifying islands of trees (Silva and Wilkinson 2021)
<doi:10.1093/sysbio/syab015>,
for calculating the median of sets of trees,
and for computing the information content of trees and splits.

Martin R. Smith

TreeDist

Calculate and Map Distances Between Phylogenetic Trees

Roy Jonker

Yong Yang

Yi Cao

CalculateTreeDistance function

<dl><dt>Func</dt>
<dd>Tree distance function.</dd>
<dt>tree1, tree2</dt>
<dd>Trees of class <code>phylo</code>, with leaves labelled identically,
or lists of such trees to undergo pairwise comparison. Where implemented,
<code>tree2 = NULL</code> will compute distances between each pair of trees in the list
<code>tree1</code> using a fast algorithm based on
Day1985;textualTreeDist.</dd>
<dt>reportMatching</dt>
<dd>Logical specifying whether to return the clade
matchings as an attribute of the score.</dd>
<dt>...</dt>
<dd>Additional arguments to <code>Func</code>.</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=TreeDist&version=2.9.2" data-mini-rdoc="TreeDist::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

Wrapper for tree distance calculations — CalculateTreeDistance

<dl>

<dt>Func</dt>
<dd>Tree distance function.</dd>


<dt>tree1, tree2</dt>
<dd>Trees of class <code>phylo</code>, with leaves labelled identically,
or lists of such trees to undergo pairwise comparison. Where implemented,
<code>tree2 = NULL</code> will compute distances between each pair of trees in the list
<code>tree1</code> using a fast algorithm based on
Day1985;textualTreeDist.</dd>


<dt>reportMatching</dt>
<dd>Logical specifying whether to return the clade
matchings as an attribute of the score.</dd>


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

CalculateTreeDistance: Wrapper for tree distance calculations

Description

Usage

Arguments

Author