SplitwiseInfo

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

<p>Sum the phylogenetic information content for all splits within a
phylogenetic tree.  This value will be greater than the total information
content of the tree where a tree contains multiple splits, as
these splits will contain mutual information.</p>

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>.
Calculates the median of a set of trees under any distance metric.

Martin R. Smith

TreeDist

Distances Between Phylogenetic Trees

SplitwiseInfo: Information content of splits within a tree

Description

Usage

Arguments

See Also

Examples