Phylogenetic networks: concepts, algorithms and applications
Gespeichert in:
| Hauptverfasser: | , , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Cambridge [u.a.]
Cambridge Univ. Press
2010
|
| Ausgabe: | 1. publ. |
| Schlagworte: | |
| Online-Zugang: | Cover image Inhaltsverzeichnis |
| Beschreibung: | Hier auch später erschienene, unveränderte Nachdrucke |
| Beschreibung: | XII, 362 S. zahlr. graph. Darst. |
| ISBN: | 9780521755962 |
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Datensatz im Suchindex
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| adam_text | IMAGE 1
PHYLOGENETIC NETWORKS
CONCEPTS, ALGORITHMS AND APPLICATIONS
DANIEL H. HUSON EBERHARD-KARLS-UNIVERSITAT TUBINGEN, GERMANY
REGULA RUPP
EBERHARD-KARLS-UNIVERSITAT TUBINGEN, GERMANY
CELINE SCORNAVACCA
EBERHARD-KARLS-UNIVERSITAT TUBINGEN, GERMANY
CAMBRIDGE UNIVERSITY PRESS
IMAGE 2
CONTENTS
PREFACE PAGE IX
PART I INTRODUCTION 1
3 3 7 8 9
11
13
13 13 20
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
1 BASICS
L.L 1.2 1.3
1.4 1.5 1.6
2 SEQUENCE
2.1 2.2 2.3
OVERVIEW UNDIRECTED AND DIRECTED GRAPHS TREES ROOTED DAGS TRAVERSALS OF
TREES AND DAGS
TAXA, CLUSTERS, CLADES AND SPLITS
ALIGNMENT
OVERVIEW PAIRWISE SEQUENCE ALIGNMENT MULTIPLE SEQUENCE ALIGNMENT
3 PHYLOGENETIC TREES
IMAGE 3
VI CONTENTS
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
127 128 132 133
138 140
6.1 6.2 6.3 6.4
6.5 6.6
OVERVIEW CLUSTERS, COMPATIBILITY AND INCOMPATIBILITY HASSE DIAGRAMS
CLUSTER NETWORKS ROOTED PHYLOGENETIC NETWORKS THE LOWEST STABLE ANCESTOR
IMAGE 4
VII CONTENTS
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
193 194 198 201 210
216
216 216 218 219 223 227 232
233 240
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
8.1 8.2 8.3 8.4
8.5
CLUSTER NETWORKS DIVIDE-AND-CONQUER USING DECOMPOSITION GALLED TREES
GALLED NETWORKS LEVEL- K NETWORKS
9 PHYLOGENETIC NETWORKS FROM SEQUENCES
9.1 9.2 9.3 9.4
9.5 9.6 9.7 9.8 9.9
CONDENSED ALIGNMENTS BINARY SEQUENCES AND SPLITS PARSIMONY SPLITS MEDIAN
NETWORKS
QUASI-MEDIAN NETWORKS MEDIAN-JOINING PRUNED QUASI-MEDIAN NETWORKS
RECOMBINATION NETWORKS GALLED TREES
10 PHYLOGENETIC NETWORKS FROM DISTANCES
IMAGE 5
VIII CONTENTS
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 SPHT 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
PHYLOGENETIC NETWORKS FROM TRIPLES OR QUARTETS 300
12.1 TREES FROM ROOTED TRIPLES 300
12.2 LEVEL-/C NETWORKS FROM ROOTED TRIPLES 302
12.3 THE QUARTET-NET METHOD 308
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
SOFTWARE 332
14.1 SPLITSTREE 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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| publisher | Cambridge Univ. Press |
| record_format | marc |
| spelling | Huson, Daniel 1960- Verfasser (DE-588)132217961 aut Phylogenetic networks concepts, algorithms and applications Daniel H. Huson ; Regula Rupp ; Celine Scornavacca 1. publ. Cambridge [u.a.] Cambridge Univ. Press 2010 XII, 362 S. zahlr. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Hier auch später erschienene, unveränderte Nachdrucke Datenverarbeitung Mathematik Cladistic analysis Data processing Cladistic analysis Mathematics Phylogeny Datenverarbeitung (DE-588)4011152-0 gnd rswk-swf Phylogenie (DE-588)4076110-1 gnd rswk-swf Methode (DE-588)4038971-6 gnd rswk-swf Phylogenetische Systematik (DE-588)4174592-9 gnd rswk-swf Evolution (DE-588)4071050-6 gnd rswk-swf Genanalyse (DE-588)4200230-8 gnd rswk-swf Mathematisches Modell (DE-588)4114528-8 gnd rswk-swf Phylogenetische Systematik (DE-588)4174592-9 s Datenverarbeitung (DE-588)4011152-0 s DE-604 Mathematisches Modell (DE-588)4114528-8 s Methode (DE-588)4038971-6 s DE-188 Phylogenie (DE-588)4076110-1 s Evolution (DE-588)4071050-6 s Genanalyse (DE-588)4200230-8 s Rupp, Regula Verfasser (DE-588)143188860 aut Scornavacca, Celine Verfasser (DE-588)143188887 aut http://assets.cambridge.org/97805217/55962/cover/9780521755962.jpg Cover image HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=021149998&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Huson, Daniel 1960- Rupp, Regula Scornavacca, Celine Phylogenetic networks concepts, algorithms and applications Datenverarbeitung Mathematik Cladistic analysis Data processing Cladistic analysis Mathematics Phylogeny Datenverarbeitung (DE-588)4011152-0 gnd Phylogenie (DE-588)4076110-1 gnd Methode (DE-588)4038971-6 gnd Phylogenetische Systematik (DE-588)4174592-9 gnd Evolution (DE-588)4071050-6 gnd Genanalyse (DE-588)4200230-8 gnd Mathematisches Modell (DE-588)4114528-8 gnd |
| subject_GND | (DE-588)4011152-0 (DE-588)4076110-1 (DE-588)4038971-6 (DE-588)4174592-9 (DE-588)4071050-6 (DE-588)4200230-8 (DE-588)4114528-8 |
| title | Phylogenetic networks concepts, algorithms and applications |
| title_auth | Phylogenetic networks concepts, algorithms and applications |
| title_exact_search | Phylogenetic networks concepts, algorithms and applications |
| title_full | Phylogenetic networks concepts, algorithms and applications Daniel H. Huson ; Regula Rupp ; Celine Scornavacca |
| title_fullStr | Phylogenetic networks concepts, algorithms and applications Daniel H. Huson ; Regula Rupp ; Celine Scornavacca |
| title_full_unstemmed | Phylogenetic networks concepts, algorithms and applications Daniel H. Huson ; Regula Rupp ; Celine Scornavacca |
| title_short | Phylogenetic networks |
| title_sort | phylogenetic networks concepts algorithms and applications |
| title_sub | concepts, algorithms and applications |
| topic | Datenverarbeitung Mathematik Cladistic analysis Data processing Cladistic analysis Mathematics Phylogeny Datenverarbeitung (DE-588)4011152-0 gnd Phylogenie (DE-588)4076110-1 gnd Methode (DE-588)4038971-6 gnd Phylogenetische Systematik (DE-588)4174592-9 gnd Evolution (DE-588)4071050-6 gnd Genanalyse (DE-588)4200230-8 gnd Mathematisches Modell (DE-588)4114528-8 gnd |
| topic_facet | Datenverarbeitung Mathematik Cladistic analysis Data processing Cladistic analysis Mathematics Phylogeny Phylogenie Methode Phylogenetische Systematik Evolution Genanalyse Mathematisches Modell |
| url | http://assets.cambridge.org/97805217/55962/cover/9780521755962.jpg http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=021149998&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT husondaniel phylogeneticnetworksconceptsalgorithmsandapplications AT ruppregula phylogeneticnetworksconceptsalgorithmsandapplications AT scornavaccaceline phylogeneticnetworksconceptsalgorithmsandapplications |