ArticlePloS one2018
Sound Colless-like balance indices for multifurcating trees.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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12 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference.Systematic biology · 2024Pooled it
- Tree balance in phylogenetic models.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Labelled histories with multifurcation and simultaneity.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- For Someone, You Are the Whole World: Host-Specificity ofInternational journal of molecular sciences · 2023Article
- The man, the plant, and the insect: shooting host specificity determinants inFrontiers in microbiology · 2023Article
- Robust, Universal Tree Balance Indices.Systematic biology · 2022Article
- Spatial structure governs the mode of tumour evolution.Nature ecology & evolution · 2022Article
- Explicit solution of divide-and-conquer dividing by a half recurrences with polynomial independent term.PloS one · 2022Article
- On the Colijn-Plazzotta numbering scheme for unlabeled binary rooted trees.Discrete applied mathematics (Amsterdam, Netherlands : 1988) · 2021Article
- On the minimum value of the Colless index and the bifurcating trees that achieve it.Journal of mathematical biology · 2020Article
- On Sackin's original proposal: the variance of the leaves' depths as a phylogenetic balance index.BMC bioinformatics · 2020Article
- A balance index for phylogenetic trees based on rooted quartets.Journal of mathematical biology · 2019Article
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3 authors.
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Abstract
The Colless index is one of the most popular and natural balance indices for bifurcating phylogenetic trees, but it makes no sense for multifurcating trees. In this paper we propose a family of Colless-like balance indices [Formula: see text] that generalize the Colless index to multifurcating phylogenetic trees. Each [Formula: see text] is determined by the choice of a dissimilarity D and a weight function [Formula: see text]. A balance index is sound when the most balanced phylogenetic trees according to it are exactly the fully symmetric ones. Unfortunately, not every Colless-like balance index is sound in this sense. We prove then that taking f(n) = ln(n + e) or f(n) = en as weight functions, the resulting index [Formula: see text] is sound for every dissimilarity D. Next, for each one of these two functions f and for three popular dissimilarities D (the variance, the standard deviation, and the mean deviation from the median), we find the most unbalanced phylogenetic trees according to [Formula: see text] with any given number n of leaves. The results show that the growth pace of the function f influences the notion of "balance" measured by the indices it defines. Finally, we introduce our R package "CollessLike," which, among other functionalities, allows the computation of Colless-like indices of trees and their comparison to their distribution under Chen-Ford-Winkel's α-γ-model for multifurcating phylogenetic trees. As an application, we show that the trees in TreeBASE do not seem to follow either the uniform model for multifurcating trees or the α-γ-model, for any values of α and γ.
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