Huson D.H. Phylogenetic networks: concepts, algorithms and applications (Cambridge, 2011). - ОГЛАВЛЕНИЕ / CONTENTS
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ОбложкаHuson D.H. Phylogenetic networks: concepts, algorithms and applications / D.H.Huson, R.Rupp, C.Scornavacca. - Cambridge: Cambridge University Press, 2011. - xii, 362 p.: ill. - Ref.: p.343-357. - Ind.: p.358-362. - ISBN 978-0-521-75596-2
 

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Оглавление / Contents
 
   Preface ..................................................... ix

Part I Introduction ............................................. l

1  Basics ....................................................... 3
   1.1  Overview ................................................ 3
   1.2  Undirected and directed graphs .......................... 3
   1.3  Trees ................................................... 7
   1.4  Rooted DAGs ............................................. 8
   1.5  Traversals of trees and DAGs ............................ 9
   1.6  Taxa, clusters, clades and splits ...................... 11

2  Sequence alignment .......................................... 13
   2.1  Overview ............................................... 13
   2.2  Pairwise sequence alignment ............................ 13
   2.3  Multiple sequence alignment ............................ 20

3  Phylogenetic trees .......................................... 23
   3.1  Overview ............................................... 23
   3.2  Phylogenetic trees ..................................... 24
   3.3  The number of phylogenetic trees ....................... 27
   3.4  Models of DNA evolution ................................ 29
   3.5  The phylogenetic tree reconstruction problem ........... 32
   3.6  Sequence-based methods ................................. 33
   3.7  Maximum parsimony ...................................... 33
   3.8  Branch-swapping methods ................................ 37
   3.9  Maximum likelihood estimation .......................... 40
   3.10 Bootstrap analysis ..................................... 43
   3.11 Bayesian methods ....................................... 45
   3.12 Distance-based methods ................................. 50
   3.13 UPGMA .................................................. 52
   3.14 Neighbor-joining ....................................... 54
   3.15 Balanced minimum evolution ............................. 56
   3.16 Comparing trees ........................................ 60
   3.17 Consensus trees ........................................ 63
   3.18 The Newick format ...................................... 66

4  Introduction to phylogenetic networks ....................... 68
   4.1  Overview ............................................... 69
   4.2  What is a phylogenetic network? ........................ 69
   4.3  Unrooted phylogenetic networks ......................... 71
   4.4  Rooted phylogenetic networks ........................... 76
   4.5  The extended Newick format ............................. 81
   4.6  Which types of networks are currently used in
        practice? .............................................. 83

Part II Theory ................................................. 85

5  Splits and unrooted phylogenetic networks ................... 87
   5.1  Overview ............................................... 87
   5.2  Splits ................................................. 88
   5.3  Compatibility and incompatibility ...................... 90
   5.4  Splits and clusters .................................... 91
   5.5  Split networks ......................................... 93
   5.6  The canonical split network ............................ 97
   5.7  Circular splits and planar split networks ............. 102
   5.8  Weak compatibility .................................... 105
   5.9  The split decomposition ............................... 107
   5.10 Representing trees in a split network ................. 121
   5.11 Comparing split networks .............................. 122
   5.12 T-theory .............................................. 122

6  Clusters and rooted phylogenetic networks .................. 127
   6.1  Overview .............................................. 127
   6.2  Clusters, compatibility and incompatibility ........... 128
   6.3  Hasse diagrams ........................................ 132
   6.4  Cluster networks ...................................... 133
   6.5  Rooted phylogenetic networks .......................... 138
   6.6  The lowest stable ancestor ............................ 140
   6.7  Representing trees in rooted networks ................. 144
   6.8  Hardwired and softwired clusters ...................... 146
   6.9  Minimum rooted phylogenetic networks .................. 149
   6.10 Decomposability ....................................... 150
   6.11 Topological constraints on rooted networks ............ 156
   6.12 Cluster containment in rooted networks ................ 168
   6.13 Tree containment ...................................... 171
   6.14 Comparing rooted networks ............................. 171

Part III Algorithms and applications .......................... 185

7  Phylogenetic networks from splits .......................... 187
   7.1  The convex hull algorithm ............................. 187
   7.2  The circular network algorithm ........................ 190

8  Phylogenetic networks from clusters ........................ 193
   8.1  Cluster networks ...................................... 193
   8.2  Divide-and-conquer using decomposition ................ 194
   8.3  Galled trees .......................................... 198
   8.4  Galled networks ....................................... 201
   8.5  Level-к networks ...................................... 210

9  Phylogenetic networks from sequences ....................... 216
   9.1  Condensed alignments .................................. 216
   9.2  Binary sequences and splits ........................... 216
   9.3  Parsimony splits ...................................... 218
   9.4  Median networks ....................................... 219
   9.5  Quasi-median networks ................................. 223
   9.6  Median-joining ........................................ 227
   9.7  Pruned quasi-median networks .......................... 232
   9.8  Recombination networks ................................ 233
   9.9  Galled trees .......................................... 240

10 Phylogenetic networks from distances ....................... 250
   10.1 Distances and splits .................................. 250
   10.2 Minimum spanning networks ............................. 251
   10.3 Split decomposition ................................... 251
   10.4 Neighbor-net .......................................... 254
   10.5 T-Rex ................................................. 261

11 Phylogenetic networks from trees ........................... 265
   11.1 Consensus split networks .............................. 265
   11.2 Consensus super split networks for unrooted trees ..... 268
   11.3 Distortion-filtered super split networks for 
        unrooted trees ........................................ 273
   11.4 Consensus cluster networks for rooted trees ........... 274
   11.5 Minimum hybridization networks ........................ 275
   11.6 Minimum hybridization networks and galled trees ....... 285
   11.7 Networks from multi-labeled trees ..................... 287
   11.8 DLT reconciliation of gene and species trees .......... 289

12 Phylogenetic networks from triples or quartets ............. 300
   12.1 Trees from rooted triples ............................. 300
   12.2 Level-fc networks from rooted triples ................. 302
   12.3 The quartet-net method ................................ 308

13 Drawing phylogenetic networks .............................. 312
   13.1 Overview .............................................. 312
   13.2 Cladograms for rooted phylogenetic trees .............. 312
   13.3 Cladograms for rooted phylogenetic networks ........... 316
   13.4 Phylograms for rooted phylogenetic trees .............. 323
   13.5 Phylograms for rooted phylogenetic networks ........... 324
   13.6 Drawing rooted phylogenetic networks with transfer
        edges ................................................. 327
   13.7 Radial diagrams for unrooted trees .................... 328
   13.8 Radial diagrams for split networks .................... 329

14 Software ................................................... 332
   14.1 Splits Tree ........................................... 332
   14.2 Network ............................................... 333
   14.3 TCS ................................................... 334
   14.4 Dendroscope ........................................... 334
   14.5 Other programs ........................................ 335

   Glossary ................................................... 338
   References ................................................. 343
   Index ...................................................... 358


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