CHAPTER 14 Tree Set Visualization, Exploration, and Applications

Chapters in this book

1. Frontmatter i
2. Short Contents vii
3. Preface xvii
4. Acknowledgments xix
5. Contributors xxi
6. CHAPTER 1 Introduction to Species Tree Inference 1
7. PART I Analytical and Methodological Developments
8. Introduction 15
9. CHAPTER 2 Large-Scale Species Tree Estimation 19
10. CHAPTER 3 Species Tree Estimation Using ASTRAL: Practical Considerations 43
11. CHAPTER 4 Species Tree Estimation Using Site Pattern Frequencies 68
12. CHAPTER 5 Practical Aspects of Phylogenetic Network Analysis Using PhyloNet 89
13. CHAPTER 6 Network Thinking: Novel Inference Tools and Scalability Challenges 120
14. PART II Empirical Inference
15. Introduction 145
16. CHAPTER 7 Phylogenomic Conflict in Plants 149
17. CHAPTER 8 Hybridization in Iochroma 161
18. CHAPTER 9 Hybridization and Polyploidy in Penstemon 175
19. CHAPTER 10 Comparison of Linked versus Unlinked Character Models for Species Tree Inference 191
20. PART III Beyond the Species Tree
21. Introduction 211
22. CHAPTER 11 The Unfinished Synthesis of Comparative Genomics and Phylogenetics: Examples from Flightless Birds 215
23. CHAPTER 12 Phylogenetic Analysis under Heterogeneity and Discordance 232
24. CHAPTER 13 The Multispecies Coalescent in Space and Time 251
25. CHAPTER 14 Tree Set Visualization, Exploration, and Applications 260
26. Bibliography 277
27. Index 317