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Finding islands of phylogenetic trees

Martin R. Smith

Collections of phylogenetic trees, such as those output by Bayesian or parsimony analysis, may occupy discrete regions of tree space such that individual clusters of trees are separated from all other trees by a certain distance. Finding such islands, and taking their consensus, can be an effective way of summarising conflicting signal in a phylogenetic dataset (Silva & Wilkinson, 2021).

# Load required libraries
library("TreeTools", quietly = TRUE)
library("TreeDist")

# Generate a set of trees
trees <- as.phylo(as.TreeNumber(BalancedTree(16)) + 0:100 - 15, 16)

Silva, A. S., & Wilkinson, M. (2021). On defining and finding islands of trees and mitigating large island bias. Systematic Biology, 70(6), 1282–1294. doi: 10.1093/sysbio/syab015

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