 |
Phylogenetic networks : concepts, algorithms and applications / by Daniel H. Huson, Regula Rupp, Celine Scornavacca. — Cambridge : Cambridge University Press, 2011. – (58.12405/H971) |
Contents
Contents
Preface
Part I Introduction
1 Basics
1.1 Overview
1.2 Undirected and directed graphs
1.3 Trees
1.4 Rooted DAGs
1.5 Traversals of trees and DAGs
1.6 Taxa， clusters， clades and splits
2 Sequence alignment
2.1 Overview
2.2 Pairwise sequence alignment
2.3 Multiple sequence alignment
3 Phylogenetic trees
3.1 Overview
3.2 Phylogenetic trees
3.3 The number of phylogenetic trees
3.4 Models of DNA evolution
3.5 The phylogenetic tree reconstruction problem
3.6 Sequence-based methods
3.7 Maximum parsimony
3.8 Branch-swapping methods
3.9 Maximum likelihood estimation
3.10 Bootstrap analysis
3.11 Bayesian methods
3.12 Distance-based methods
3.13 UPGMA
3.14 Neighbor-joining
3.15 Balanced minimum evolution
3.16 Comparing trees
3.17 Consensus trees
3.18 The Newick format
4 Introduction to phylogenetic networks
4.1 Overview
4.2 What is a phylogenetic network?
4.3 Unrooted phylogenetic networks
4.4 Rooted phylogenetic networks
4.5 The extended Newick format
4.6 Which types of networks are currently used in practice?
Part II Theory
5 Splits and unrooted phylogenetic networks
5.1 Overview
5.2 Splits
5.3 Compatibility and incompatibility
5.4 Splits and clusters
5.5 Split networks
5.6 The canonical split network
5.7 Circular splits and planar split networks
5.8 Weak compatibility
5.9 The split decomposition
5.10 Representing trees in a split network
5.11 Comparing split networks
5.12 T-theory
6 Clusters and rooted phylogenetic networks
6.1 Overview
6.2 Clusters， compatibility and incompatibility
6.3 Hasse diagrams
6.4 Cluster networks
6.5 Rooted phylogenetic networks
6.6 The lowest stable ancestor
6.7 Representing trees in rooted networks
6.8 Hardwired and softwired clusters
6.9 Minimum rooted phylogenetic networks
6.10 Decomposability
6.11 Topological constraints on rooted networks
6.12 Cluster containment in rooted networks
6.13 Tree containment
6.14 Comparing rooted networks
Part III Algorithms and applications
7 Phylogenetic networks from splits
7.1 The convex hull algorithm
7.2 The circular network algorithm
8 Phylogenetic networks from clusters
8.1 Cluster networks
8.2 Divide-and-conquer using decomposition
8.3 Galled trees
8.4 Galled networks
8.5 Level-k networks
9 Phylogenetic networks from sequences
9.1 Condensed alignments
9.2 Binary sequences and splits
9.3 Parsimony splits
9.4 Median networks
9.5 Quasi-median networks
9.6 Median-joining
9.7 Pruned quasi-median networks
9.8 Recombination networks
9.9 Galled trees
10 Phylogenetic networks from distances
10.1 Distances and splits
10.2 Minimum spanning networks
10.3 Split decomposition
10.4 Neighbor-net
10.5 T-Rex
11 Phylogenetic networks from trees
11.1 Consensus split networks
11.2 Consensus super split networks for unrooted trees
11.3 Distortion-filtered super split networks for unrooted trees
11.4 Consensus cluster networks for rooted trees
11.5 Minimum hybridization networks
11.6 Minimum hybridization networks and galled trees
11.7 Networks from multi-labeled trees
11.8 DLT reconciliation of gene and species trees
12 Phylogenetic networks from triples or quartets
12.1 Trees from rooted triples
12.2 Level-k networks from rooted triples
12.3 The quartet-net method
13 Drawing phylogenetic networks
13.1 Overview
13.2 Cladograms for rooted phylogenetic trees
13.3 Cladograms for rooted phylogenetic networks
13.4 Phylograms for rooted phylogenetic trees
13.5 Phylograms for rooted phylogenetic networks
13.6 Drawing rooted phylogenetic networks with transfer edges
13.7 Radial diagrams for unrooted trees
13.8 Radial diagrams for split networks
14 Software
14.1 SplitsTree
14.2 Network
14.3 TCS
14.4 Dendroscope
14.5 Other programs
Glossary
References
Index
