『Basic Phylogenetic Combinatorics』

Andreas Dress, Katharina T. Huber, Jacobus Koolen, Vincent Moulton, and Andreas Spillner

(2012年刊行,Cambridge University Press, Cambridge, xii+264 pp., ISBN:9780521768320 [hbk] / ISBN:9781139210775 [eBook] → 版元ページ

【目次】
Preface ix

1. Preliminaries 1

1.1 Sets, set systems, and partially ordered sets 1
1.2 Graphs 4
1.3 Metric spaces 13
1.4 Computational complexity 19

2. Encoding X-trees 21

2.1 X-trees 21
2.2 Encoding X-trees with splits 23
2.3 Encoding X-trees with metrics 26
2.4 Encoding X-trees with quartets 27

3. Consistency of X-trees encodings 31

3.1 The 4-point condition 31
3.2 Compatibility 38
3.3 Quartet systems 42

4. From split systems to networks 50

4.1 The Buneman graph 51
4.2 The Buneman graph of a compatible split system 59
4.3 Median networks 63
4.4 Split netwotks 65
4.5 Split graphs and metrics: The theory of X-nets 72

5. From metrics to networks: The tight span 75

5.1 The tight span 75
5.2 A canonical contraction from P(D) onto T(D) 82
5.3 The tight span of a finite metric space 87
5.4 Networks from tight spans 93
5.5 Network realizations of metrics 97
5.6 Optimal and hereditarily optimal realizations 100

6. From quartet and tree systems to trees 104

6.1 On quartet systems 105
6.2 On set and tree systems 113
6.3 Costructing from trees from quartet, tree, and set systems 118
6.4 Slim tree systems 121
6.5 Definitive set systems 128

7. From metrics to split systems and back 137

7.1 Buneman splits 137
7.2 Weakly compatible split systems 146
7.3 From weighted split systems to bivariate maps 161
7.4 The Buneman complex and the tight span 167

8. Maps to and from quartet systems 171

8.1 A Galois connection between split and quartet systems 171
8.2 A map from quartets to metrics 177
8.3 Transitive quartet systems 180

9. Rooted trees and the Farris transform 195

9.1 Rooted X-trees, clusters, and tights 198
9.2 Dated rooted X-trees and hierarchical dissimilarities 202
9.3 Affine versus projective clustering and the combinatorial Farris transform 205
9.4 Hierarchical dissimilarities, hyperbolic maps, and their Farris transform 209
9.5 Hierarchical dissimilarities, generalized metrics, and the tight-span construction 214
9.6 Algorithmic issues 218

10. On measuring and removing inconsistencies 222

10.1 k-compatibility 222
10.2 Δ-hierarchical approximations 230
10.3 Quartet-Joining and QNet 236


Commonly used symbols 242
Bibliography 253
Index 261

すでに Leo van Iersel による詳しい書評が書かれている: Systematic Biology, 62(2):346–348, 2013 extract