Calculate and Map Distances Between Phylogenetic Trees
Description
Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
,
including the Nye et al. (2006) metric ;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance , and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) .
Includes tools for visualizing mappings of tree space (Smith 2022)
,
for identifying islands of trees (Silva and Wilkinson 2021)
,
for calculating the median of sets of trees,
and for computing the information content of trees and splits.