ArticleJournal of mathematical biology2021
Computing nearest neighbour interchange distances between ranked phylogenetic trees.
Article in Journal of mathematical biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 4 citations in OpenAlex.
- Antifungal activity of Burkholderia sensu lato metabolites against coffee phytopathogens: evidence of chemical diversity.World journal of microbiology & biotechnology · 2026Article
- Spaces of ranked tree-child networks.Journal of mathematical biology · 2025Article
- Phylo-rs: an extensible phylogenetic analysis library in rust.BMC bioinformatics · 2025Article
- A vector representation for phylogenetic trees.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Estimating the mean in the space of ranked phylogenetic trees.Bioinformatics (Oxford, England) · 2024Article
- Ranked Subtree Prune and Regraft.Bulletin of mathematical biology · 2024Article
- Artificial intelligence and bioinformatics: a journey from traditional techniques to smart approaches.Gastroenterology and hepatology from bed to bench · 2024Review
- Leaping through Tree Space: Continuous Phylogenetic Inference for Rooted and Unrooted Trees.Genome biology and evolution · 2023Article
- Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data.Journal of computational biology : a journal of computational molecular cell biology · 2023Article
- StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent.Systematic biology · 2022Article
- Discrete coalescent trees.Journal of mathematical biology · 2021Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many popular algorithms for searching the space of leaf-labelled (phylogenetic) trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are given by pairs of trees connected by one rearrangement operation (sometimes called a move). Most popular are the classical nearest neighbour interchange, subtree prune and regraft, and tree bisection and reconnection moves. The problem of computing distances, however, is [Formula: see text]-hard in each of these graphs, making tree inference and comparison algorithms challenging to design in practice. Although anked phylogenetic trees are one of the central objects of interest in applications such as cancer research, immunology, and epidemiology, the computational complexity of the shortest path problem for these trees remained unsolved for decades. In this paper, we settle this problem for the ranked nearest neighbour interchange operation by establishing that the complexity depends on the weight difference between the two types of tree rearrangements (rank moves and edge moves), and varies from quadratic, which is the lowest possible complexity for this problem, to [Formula: see text]-hard, which is the highest. In particular, our result provides the first example of a phylogenetic tree rearrangement operation for which shortest paths, and hence the distance, can be computed efficiently. Specifically, our algorithm scales to trees with tens of thousands of leaves (and likely hundreds of thousands if implemented efficiently).
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