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  Tree balance indices: a comprehensive survey

Fischer, M., Herbst, L., Kersting, S., Kühn, A. L., & Wicke, K. (2023). Tree balance indices: a comprehensive survey. Cham: Springer Cham. doi:10.1007/978-3-031-39800-1.

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 Urheber:
Fischer, Mareike, Autor
Herbst, Lina1, Autor                 
Kersting, Sophie, Autor
Kühn, Annemarie Luise, Autor
Wicke, Kristina, Autor
Affiliations:
1Transmission, Infection, Diversification & Evolution Group (tide), Max Planck Institute of Geoanthropology, Max Planck Society, ou_3508663              

Inhalt

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Schlagwörter: phylogenetics, tree balance, Yule model, Search trees, Colless index, Sackin index, Total Cophenetic index, Uniform model
 Zusammenfassung: Whether you are looking for an introduction to the field of tree balance, a reference work on the multitude of available balance indices or inspiration for your future research, this book offers all three. It delves into the significance of tree balance in phylogenetics and other research domains, where numerous indices have been introduced over the years. While the variations in definitions and underlying principles among these indices have long remained a challenge, this survey addresses the problem by presenting formal definitions of balance and imbalance indices and establishing desirable properties.

The book is comprehensive both in the inclusion of a variety of indices and in the information provided on them: the authors meticulously analyze and categorize established indices, shedding light on their general, statistical and combinatorial properties. They reveal that, while some known balance indices fail to meet the most basic criteria, certain tree shape statistics from other contexts prove to be effective balance measures. The collected properties are neatly presented, numerous new results are established, open research questions are highlighted, and possible applications are discussed.

Reviewing over twenty (im)balance indices, a wealth of mathematical insights is provided, accompanied by real-world examples showcasing the importance of tree balance in diverse research areas. Catering to researchers, students, mathematicians, and biologists, the book can be used as a textbook for university seminars, a reference on tree balance, and as a source of inspiration for future research. It is accompanied by the free R package 'treebalance', a powerful tool to further explore and apply the discussed concepts, and a website allowing quick access to the main information and the latest developments in the field.

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Sprache(n): eng - English
 Datum: 2023-10-312023-11-01
 Publikationsstatus: Erschienen
 Seiten: XV, 404 p.
 Ort, Verlag, Ausgabe: Cham : Springer Cham
 Inhaltsverzeichnis: Part I Introduction
1 Opening remarks
2 Preliminaries
2.1 General notation and concepts
2.2 Rooted trees and related concepts
2.3 Ordering and enumerating rooted (binary) trees
2.4 Probabilistic models of phylogenetic trees
3 A brief sketch on the relevance and history of tree balance
4 Concepts of tree balance and imbalance
4.1 Definition of tree balance and imbalance
4.2 General, combinatorial and statistical properties
Part II Tree balance and imbalance indices
5 Sackin index
6 Average leaf depth
7 Variance of leaf depths
8 Total cophenetic index
9 b𝒔-shape statistic
10 𝑩1 index
11 𝑩2 index
12 Colless index
13 Corrected Colless index
14 Equal weights Colless index / 𝑰2 index
15 Quadratic Colless index
16 Colless-like indices
17 𝑰-based indices
18 Symmetry nodes index
19 Rogers 𝑱 index
20 Rooted quartet index
21 Colijn-Plazzotta rank
22 Furnas rank
23 Less established tree shape statistics that are (im)balance indices
23.1 Total internal path length
23.2 Total path length
23.3 Average (vertex) depth
23.4 Maximum depth
23.5 Maximum width
23.6 Modified maximum difference in widths
23.7 Maximum width over maximum depth
23.8 stairs1
23.9 stairs2
24 Related tree shape statistics that are not (im)balance indices
24.1 Diameter, area per pair index, and the Wiener index
24.2 Farness and betweenness centrality
24.3 Degree of root imbalance, I value, and the mean 𝐼′10 index
24.4 D index
24.5 Maximum difference in widths
24.6 Cherry index and modified cherry index
24.7 ILnumber and ladder length
24.8 Number of pitchforks, double cherries, 4-caterpillars and clades of
size x
25 Extended and alternative measures of tree balance
25.1 Obtaining new balance indices from established indices
25.2 Normalizing (im)balance indices
25.3 Alternative ways of measuring tree balance
Part III Applications and outlook
26 Software
26.1 Existing software packages
26.2 The software package treebalance
26.3 Examples for the usage of treebalance
26.3.1 Implementing the uniform model based on the Furnas rank
and the symmetry nodes index
26.3.2 Uncovering divergence from expected imbalance
26.3.3 Exploring the range and number of distinct (im)balance
index values
27 Applications
28 Discussion and outlook
28.1 Summary and discussion
28.2 Directions for future research
A Lookup Tables
References
List of symbols
Index
 Art der Begutachtung: -
 Identifikatoren: DOI: 10.1007/978-3-031-39800-1
ISBN: 978-3-031-39799-8
ISBN: 978-3-031-39802-5
ISBN: 978-3-031-39800-1
Anderer: gea0219
 Art des Abschluß: -

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