Inferring phylogenies:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Sunderland, Mass.
Sinauer
2004
|
| Ausgabe: | 1. edition |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XX, 664 Seiten Illustrationen, Diagramme |
| ISBN: | 9780878931774 0878931775 |
Internformat
MARC
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| 100 | 1 | |a Felsenstein, Joseph |d 1942- |e Verfasser |0 (DE-588)141921552 |4 aut | |
| 245 | 1 | 0 | |a Inferring phylogenies |c Joseph Felsenstein |
| 250 | |a 1. edition | ||
| 264 | 1 | |a Sunderland, Mass. |b Sinauer |c 2004 | |
| 300 | |a XX, 664 Seiten |b Illustrationen, Diagramme | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 4 | |a Analyse cladistique - Mathématiques | |
| 650 | 7 | |a Análises cladística |2 larpcal | |
| 650 | 7 | |a Botânica |2 larpcal | |
| 650 | 7 | |a Filogenia |2 larpcal | |
| 650 | 7 | |a Fylogenese |2 gtt | |
| 650 | 7 | |a Wiskundige methoden |2 gtt | |
| 650 | 7 | |a Árvores |2 larpcal | |
| 650 | 4 | |a Mathematik | |
| 650 | 4 | |a Cladistic analysis |x Mathematics | |
| 650 | 4 | |a Mathematics | |
| 650 | 4 | |a Phylogeny | |
| 650 | 0 | 7 | |a Baum |g Mathematik |0 (DE-588)4004849-4 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Phylogenie |0 (DE-588)4076110-1 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Mathematisches Modell |0 (DE-588)4114528-8 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Phylogenetische Systematik |0 (DE-588)4174592-9 |2 gnd |9 rswk-swf |
| 689 | 0 | 0 | |a Phylogenie |0 (DE-588)4076110-1 |D s |
| 689 | 0 | 1 | |a Phylogenetische Systematik |0 (DE-588)4174592-9 |D s |
| 689 | 0 | 2 | |a Baum |g Mathematik |0 (DE-588)4004849-4 |D s |
| 689 | 0 | 3 | |a Mathematisches Modell |0 (DE-588)4114528-8 |D s |
| 689 | 0 | |5 DE-604 | |
| 856 | 4 | 2 | |m HEBIS Datenaustausch Darmstadt |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010321469&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
Datensatz im Suchindex
| _version_ | 1805083663722872832 |
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| adam_text |
INFERRING PHYTOGENIES JOSEPH FELSENSTEIN UNIVERSITY OF WASHINGTON
SINAUER ASSOCIATES, INC. * PUBLISHERS SUNDERLAND, MASSACHUSETTS
TECHNISCHE UNIVERSITST DARMSTATII FACHBEREICH 10 * BIOIOGIE * B I BII O
T H E K * SCHNITTSPAHNSTRABE 10 D J 6 4 2 8 7 D A R RTI S T A D T
IFIY.-NR. CONTENTS PREFACE XIX 1 PARSIMONY METHODS 1 A SIMPLE EXAMPLE '.
1 EVALUATING A PARTICULAR TREE 1 ROOTEDNESS AND UNROOTEDNESS 4 METHODS
OF ROOTING THE TREE 6 BRANCH LENGTHS 8 UNRESOLVED QUESTIONS 9 2 COUNTING
EVOLUTIONARY CHANGES 11 THE FITCH ALGORITHM 11 THE SANKOFF ALGORITHM 13
CONNECTION BETWEEN THE TWO ALGORITHMS 16 USING THE ALGORITHMS WHEN
MODIFYING TREES 16 VIEWS 16 USING VIEWS WHEN A TREE IS ALTERED 17
FURTHER ECONOMIES 18 3 HOW MANY TREES ARE THERE? 19 ROOTED BIFURCATING
TREES 20 UNROOTED BIFURCATING TREES 24 MULTIFURCATING TREES . . .' 25
UNROOTED TREES WITH MULTIFURCATIONS 28 TREE SHAPES 28 ROOTED BIFURCATING
TREE SHAPES 29 ROOTED MULTIFURCATING TREE SHAPES 30 UNROOTED SHAPES 32
LABELED HISTORIES 35 PERSPECTIVE 36 VI 4 FINDING THE BEST TREE BY
HEURISTIC SEARCH 37 NEAREST-NEIGHBOR INTERCHANGES 38 SUBTREE PRUNING AND
REGRAFTING 41 TREE BISECTION AND RECONNECTION 44 OTHER TREE
REARRANGEMENT METHODS 44 TREE-FUSING 7 . 44 GENETIC ALGORITHMS 44 TREE
WINDOWS AND SECTORIAL SEARCH 46 SPEEDING UP REARRANGEMENTS 46 SEQUENTIAL
ADDITION 47 STAR DECOMPOSITION 48 TREE SPACE 48 SEARCH BY REWEIGHTING OF
CHARACTERS 51 SIMULATED ANNEALING 52 HISTORY 53 5 FINDING THE BEST TREE
BY BRANCH AND BOUND 54 A NONBIOLOGICAL EXAMPLE 54 FINDING THE OPTIMAL
SOLUTION 57 NP-HARDNESS 57 BRANCH AND BOUND METHODS 60 PHYLOGENIES:
DESPAIR AND HOPE 60 BRANCH AND BOUND FOR PARSIMONY 61 IMPROVING THE
BOUND 64 USING STILL-ABSENT STATES 64 USING COMPATIBILITY 64 RULES
LIMITING THE SEARCH 65 6 ANCESTRAL STATES AND BRANCH LENGTHS 67
RECONSTRUCTING ANCESTRAL STATES 67 ACCELERATED AND DELAYED
TRANSFORMATION *. . 70 BRANCH LENGTHS 70 7 VARIANTS OF PARSIMONY 73
CAMIN-SOKAL PARSIMONY 73 PARSIMONY ON AN ORDINAL SCALE 74 DOLLO
PARSIMONY 75 POLYMORPHISM PARSIMONY 76 UNKNOWN ANCESTRAL STATES 78
MULTIPLE STATES AND BINARY CODING 78 DOLLO PARSIMONY AND MULTIPLE STATES
80 VLL POLYMORPHISM PARSIMONY AND MULTIPLE STATES 81 TRANSFORMATION
SERIES ANALYSIS 81 WEIGHTING CHARACTERS 82 SUCCESSIVE WEIGHTING AND
NONLINEAR WEIGHTING 83 SUCCESSIVE WEIGHTING 83 NONSUCCESSIVE ALGORITHMS
". 84 8 COMPATIBILITY 87 TESTING COMPATIBILITY 88 THE PAIRWISE
COMPATIBILITY THEOREM 89 CLIQUES OF COMPATIBLE CHARACTERS 91 FINDING THE
TREE FROM THE CLIQUE 92 OTHER CASES WHERE CLIQUES CAN BE USED 94 WHERE
CLIQUES CANNOT BE USED 94 PERFECT PHYLOGENY 95 USING COMPATIBILITY ON
MOLECULES ANYWAY 96 9 STATISTICAL PROPERTIES OF PARSIMONY 97 LIKELIHOOD
AND PARSIMONY 97 THE WEIGHTS 100 UNWEIGHTED PARSIMONY 100 LIMITATIONS OF
THIS JUSTIFICATION OF PARSIMONY 101 FARRIS'S PROOFS 102 NO COMMON
MECHANISM 103 LIKELIHOOD AND COMPATIBILITY 105 PARSIMONY VERSUS
COMPATIBILITY 107 CONSISTENCY AND PARSIMONY 107 CHARACTER PATTERNS AND
PARSIMONY 107 OBSERVED NUMBERS OF THE PATTERNS 110 OBSERVED FRACTIONS OF
THE PATTERNS 110 EXPECTED FRACTIONS OF THE PATTERNS ILL INCONSISTENCY
113 WHEN INCONSISTENCY IS NOT A PROBLEM 114 THE NUCLEOTIDE SEQUENCE CASE
115 OTHER SITUATIONS WHERE CONSISTENCY IS GUARANTEED 117 DOES A
MOLECULAR CLOCK GUARANTEE CONSISTENCY? 118 THE FARRIS ZONE 120 SOME
PERSPECTIVE 121 10 A DIGRESSION ON HISTORY AND PHILOSOPHY 123 HOW
PHYLOGENY ALGORITHMS DEVELOPED 123 SOKAL AND SNEATH 123 EDWARDS AND
CAVALLI-SFORZA 125 CAMIN AND SOKAL AND PARSIMONY 128 VLLL ECK AND
DAYHOFF AND MOLECULAR PARSIMONY 130 FITCH AND MARGOLIASH POPULARIZE
DISTANCE MATRIX METHODS 131 WILSON AND LE QUESNE INTRODUCE COMPATIBILITY
133 JUKES AND CANTOR AND MOLECULAR DISTANCES 134 FARRIS AND KLUGE AND
UNORDERED PARSIMONY^ -,. 134 FITCH AND MOLECULAR PARSIMONY 136
FURTHER WORK 136 WHAT ABOUT WILLI HENNIG AND WALTER ZIMMERMAN? 136
DIFFERENT PHILOSOPHICAL FRAMEWORKS 138 HYPOTHETICO-DEDUCTIVE 138 LOGICAL
PARSIMONY 140 LOGICAL PROBABILITY? 142 CRITICISMS OF STATISTICAL
INFERENCE 143 THE IRRELEVANCE OF CLASSIFICATION 145 11 DISTANCE MATRIX
METHODS 147 BRANCH LENGTHS AND TIMES 147 THE LEAST SQUARES METHODS 148
LEAST SQUARES BRANCH LENGTHS 148 FINDING THE LEAST SQUARES TREE TOPOLOGY
153 THE STATISTICAL RATIONALE 153 GENERALIZED LEAST SQUARES 154
DISTANCES 155 THE JUKES-CANTOR MODEL*AN EXAMPLE 156 WHY CORRECT FOR
MULTIPLE CHANGES? 158 MINIMUM EVOLUTION 159 CLUSTERING ALGORITHMS , 161
UPGMA AND LEAST SQUARES 161 A CLUSTERING ALGORITHM 162 AN EXAMPLE 162
UPGMA ON NONCLOCKLIKE TREES 165 NEIGHBOR-JOINING 166 PERFORMANCE 168
USING NEIGHBOR-JOINING WITH OTHER METHODS 169 RELATION OF
NEIGHBOR-JOINING TO LEAST SQUARES 169 WEIGHTED VERSIONS OF
NEIGHBOR-JOINING 170 OTHER APPROXIMATE DISTANCE METHODS 171 DISTANCE
WAGNER METHOD 171 A RELATED FAMILY 171 MINIMIZING THE MAXIMUM
DISCREPANCY 172 TWO APPROACHES TO ERROR IN TREES 172 A PUZZLING FORMULA
173 CONSISTENCY AND DISTANCE METHODS 174 IX A LIMITATION OF DISTANCE
METHODS 175 12 QUARTETS OF SPECIES 176 THE FOUR POINT METRIC 177 THE
SPLIT DECOMPOSITION 178 RELATED METHODS 182 SHORT QUARTETS METHODS 182
THE DISK-COVERING METHOD 183 CHALLENGES FOR THE SHORT QUARTETS AND DCM
METHODS 185 THREE-TAXON STATEMENT METHODS 186 OTHER USES OF QUARTETS
WITH PARSIMONY 188 CONSENSUS SUPERTREES 189 NEIGHBORLINESS 191 DE
SOETE'S SEARCH METHOD 192 QUARTET PUZZLING AND SEARCHING TREE SPACE 193
PERSPECTIVE 194 13 MODELS OF DNA EVOLUTION 196 KIMURA'S TWO-PARAMETER
MODEL 196 CALCULATION OF THE DISTANCE 198 THE TAMURA-NEI MODEL, F84, AND
HKY 200 THE GENERAL TIME-REVERSIBLE MODEL 204 DISTANCES FROM THE GTR
MODEL 206 THE GENERAL 12-PARAMETER MODEL 210 LOGDET DISTANCES 211 OTHER
DISTANCES 213 VARIANCE OF DISTANCE 214 RATE VARIATION BETWEEN SITES OR
LOCI 215 DIFFERENT RATES AT DIFFERENT SITES 215 DISTANCES WITH KNOWN
RATES 216 DISTRIBUTION OF RATES 216 GAMMA- AND LOGNORMALLY DISTRIBUTED
RATES 217 DISTANCES FROM GAMMA-DISTRIBUTED RATES 217 MODELS WITH
NONINDEPENDENCE OF SITES 221 14 MODELS OF PROTEIN EVOLUTION 222 AMINO
ACID MODELS 222 THE DAYHOFF MODEL 222 OTHER EMPIRICALLY-BASED MODELS 223
MODELS DEPENDING ON SECONDARY STRUCTURE 225 CODON-BASED MODELS 225
INEQUALITY OF SYNONYMOUS AND NONSYNONYMOUS SUBSTITUTIONS . . . 227
PROTEIN STRUCTURE AND CORRELATED CHANGE 228 15 RESTRICTION SITES, RAPDS,
AFLPS, AND MICROSATELLITES 230 RESTRICTION SITES '. 230 NEI AND TAJIMA'S
MODEL 230 DISTANCES BASED ON RESTRICTION SITES 233 ISSUES OF
ASCERTAINMENT 234 PARSIMONY FOR RESTRICTION SITES 235 MODELING
RESTRICTION FRAGMENTS 236 PARSIMONY WITH RESTRICTION FRAGMENTS 239 RAPDS
AND AFLPS . 239 THE ISSUE OF DOMINANCE ; 240 UNRESOLVED PROBLEMS 240
MICROSATELLITE MODELS 241 THE ONE-STEP MODEL 241 MICROSATELLITE
DISTANCES 242 A BROWNIAN MOTION APPROXIMATION 244 MODELS WITH
CONSTRAINTS ON ARRAY SIZE 246 MULTI-STEP AND HETEROGENEOUS MODELS 246
SNAKES AND LADDERS 246 COMPLICATIONS 247 16 LIKELIHOOD METHODS 248
MAXIMUM LIKELIHOOD 248 AN EXAMPLE 249 COMPUTING THE LIKELIHOOD OF A TREE
251 ECONOMIZING ON THE COMPUTATION 253 HANDLING AMBIGUITY AND ERROR 255
UNROOTEDNESS 256 FINDING THE MAXIMUM LIKELIHOOD TREE 256 INFERRING
ANCESTRAL SEQUENCES 259 RATES VARYING AMONG SITES 260 HIDDEN MARKOV
MODELS 262 AUTOCORRELATION OF RATES 264 HMMS FOR OTHER ASPECTS OF MODELS
265 ESTIMATING THE STATES 265 MODELS WITH CLOCKS 266 RELAXING MOLECULAR
CLOCKS 266 MODELS FOR RELAXED CLOCKS 267 COVARIONS 268 EMPIRICAL
APPROACHES TO CHANGE OF RATES 269 ARE ML ESTIMATES CONSISTENT? 269
COMPARABILITY OF LIKELIHOODS 270 A NONEXISTENT PROOF? 270 A SIMPLE PROOF
271 XI MISBEHAVIOR WITH THE WRONG MODEL 272 BETTER BEHAVIOR WITH THE
WRONG MODEL 274 17 HADAMARD METHODS 275 THE EDGE LENGTH SPECTRUM AND
CONJUGATE SPECTRUM 279 THE CLOSEST TREE CRITERION 281 DNA MODELS 284
COMPUTATIONAL EFFORT 285 EXTENSIONS OF HADAMARD METHODS ' 286 18
BAYESIAN INFERENCE OF PHYLOGENIES 288 BAYES' THEOREM 288 BAYESIAN
METHODS FOR PHYLOGENIES 289 MARKOV CHAIN MONTE CARLO METHODS 292 THE
METROPOLIS ALGORITHM 292 ITS EQUILIBRIUM DISTRIBUTION 293 BAYESIAN MCMC
294 BAYESIAN MCMC FOR PHYLOGENIES 295 PRIORS 295 PROPOSAL DISTRIBUTIONS
296 COMPUTING THE LIKELIHOODS 298 SUMMARIZING THE POSTERIOR 299 PRIORS
ON TREES 300 CONTROVERSIES OVER BAYESIAN INFERENCE 301 UNIVERSALITY OF
THE PRIOR 301 FLAT PRIORS AND DOUBTS ABOUT THEM 301 APPLICATIONS OF
BAYESIAN METHODS 304 19 TESTING MODELS, TREES, AND CLOCKS 307 LIKELIHOOD
AND TESTS 307 LIKELIHOOD RATIOS NEAR ASYMPTOPIA 308 MULTIPLE PARAMETERS
309 SOME PARAMETERS CONSTRAINED, SOME NOT 310 CONDITIONS 310 CURVATURE
OR HEIGHT? 311 INTERVAL ESTIMATES 311 TESTING ASSERTIONS ABOUT
PARAMETERS 311 COINS IN A BARREL 313 EVOLUTIONARY RATES INSTEAD OF COINS
314 CHOOSING AMONG NONNESTED HYPOTHESES: AIC AND BIC 315 AN EXAMPLE
USING THE AIC CRITERION 317 THE PROBLEM OF MULTIPLE TOPOLOGIES 318 LRTS
AND SINGLE BRANCHES 319 INTERIOR BRANCH TESTS 320 XLL INTERIOR BRANCH
TESTS USING PARSIMONY 321 A MULTIPLE-BRANCH COUNTERPART OF INTERIOR
BRANCH TESTS 322 TESTING THE MOLECULAR CLOCK 322 PARSIMONY-BASED METHODS
322 DISTANCE-BASED METHODS 323 LIKELIHOOD-BASED METHODS 323 THE RELATIVE
RATE TEST 324 SIMULATION TESTS BASED ON LIKELIHOOD . . .* 328 FURTHER
LITERATURE 329 MORE EXACT TESTS AND CONFIDENCE INTERVALS 329 TESTS FOR
THREE SPECIES WITH A CLOCK 329 BREMER SUPPORT 330 ZANDER'S CONDITIONAL
PROBABILITY OF RECONSTRUCTION 331 MORE GENERALIZED CONFIDENCE SETS 332
20 BOOTSTRAP, JACKKNIFE, AND PERMUTATION TESTS 335 THE BOOTSTRAP AND THE
JACKKNIFE 335 BOOTSTRAPPING AND PHYLOGENIES 337 THE DELETE-HALF
JACKKNIFE 339 THE BOOTSTRAP AND JACKKNIFE FOR PHYLOGENIES 340 THE
MULTIPLE-TESTS PROBLEM 342 INDEPENDENCE OF CHARACTERS 342 IDENTICAL
DISTRIBUTION * A PROBLEM? 343 INVARIANT CHARACTERS AND RESAMPLING
METHODS . 344 BIASES IN BOOTSTRAP AND JACKKNIFE PROBABILITIES 346 P
VALUES IN A SIMPLE NORMAL CASE 346 METHODS OF REDUCING THE BIAS 349 THE
DRUG TESTING ANALOGY 352 ALTERNATIVES TO P VALUES 355 PROBABILITIES OF
TREES 356 USING TREE DISTANCES 356 JACKKNIFING SPECIES 357 PARAMETRIC
BOOTSTRAPPING 357 ADVANTAGES AND DISADVANTAGES OF THE PARAMETRIC
BOOTSTRAP 358 PERMUTATION TESTS 358 PERMUTING SPECIES WITHIN CHARACTERS
359 PERMUTING CHARACTERS 361 SKEWNESS OF TREE LENGTH DISTRIBUTION 362 21
PAIRED-SITES TESTS 364 AN EXAMPLE 365 MULTIPLE TREES 369 THE SH TEST .
." 369 OTHER MULTIPLE-COMPARISON TESTS 371 XLLL TESTING OTHER PARAMETERS
. . 372 PERSPECTIVE 372 22 INVARIANTS 373 SYMMETRY INVARIANTS 374
THREE-SPECIES INVARIANTS 376 LAKE'S LINEAR INVARIANTS 378 CAVENDER'S
QUADRATIC INVARIANTS 380 THE K INVARIANTS 380 THE L INVARIANTS 381
GENERALIZATION OF CAVENDER'S L INVARIANTS 382 DROLET AND SANKOFF'S
FC-STATE QUADRATIC INVARIANTS 385 CLOCK INVARIANTS 385 GENERAL METHODS
FOR FINDING INVARIANTS 386 FOURIER TRANSFORM METHODS 386 GROBNER BASES
AND OTHER GENERAL METHODS 387 EXPRESSIONS FOR ALL THE 3ST INVARIANTS 387
FINDING ALL INVARIANTS EMPIRICALLY 387 ALL LINEAR INVARIANTS 388 SPECIAL
CASES AND EXTENSIONS 389 INVARIANTS AND EVOLUTIONARY RATES 389 TESTING
INVARIANTS 389 WHAT USE ARE INVARIANTS? 390 23 BROWNIAN MOTION AND GENE
FREQUENCIES 391 BROWNIAN MOTION 391 LIKELIHOOD FOR A PHYLOGENY 392 WHAT
LIKELIHOOD TO COMPUTE? 395 ASSUMING A CLOCK 399 THE REML APPROACH 400
MULTIPLE CHARACTERS AND KRONECKER PRODUCTS 402 PRUNING THE LIKELIHOOD
404 MAXIMIZING THE LIKELIHOOD 406 INFERRING ANCESTRAL STATES 408
SQUARED-CHANGE PARSIMONY 409 GENE FREQUENCIES AND BROWNIAN MOTION 7 410
USING APPROXIMATE BROWNIAN MOTION 411 DISTANCES FROM GENE FREQUENCIES
412 A MORE EXACT LIKELIHOOD METHOD 413 GENE FREQUENCY PARSIMONY 413 XIV
24 QUANTITATIVE CHARACTERS 415 NEUTRAL MODELS OF QUANTITATIVE CHARACTERS
416 CHANGES DUE TO NATURAL SELECTION 419 SELECTIVE CORRELATION 419
COVARIANCES OF MULTIPLE CHARACTERS IN MULTIPLE LINEAGES 420 SELECTION
FOR AN OPTIMUM 420 BROWNIAN MOTION AND SELECTION 422 CORRECTING FOR
CORRELATIONS 422 PUNCTUATIONAL MODELS 424 INFERRING PHYLOGENIES AND
CORRELATIONS 425 CHASING A COMMON OPTIMUM 426 THE CHARACTER-CODING
"PROBLEM" 426 CONTINUOUS-CHARACTER PARSIMONY METHODS 428 MANHATTAN
METRIC PARSIMONY 428 OTHER PARSIMONY METHODS 429 THRESHOLD MODELS 429 25
COMPARATIVE METHODS 432 AN EXAMPLE WITH DISCRETE STATES 432 AN EXAMPLE
WITH CONTINUOUS CHARACTERS 433 THE CONTRASTS METHOD 435 CORRELATIONS
BETWEEN CHARACTERS 436 WHEN THE TREE IS NOT COMPLETELY KNOWN 437
INFERRING CHANGE IN A BRANCH 438 SAMPLING ERROR 439 THE STANDARD
REGRESSION AND OTHER VARIATIONS 442 GENERALIZED LEAST SQUARES 442
PHYLOGENETIC AUTOCORRELATION 442 TRANSFORMATIONS OF TIME 442 SHOULD WE
USE THE PHYLOGENY AT ALL? 443 PAIRED-LINEAGE TESTS 443 DISCRETE
CHARACTERS 444 RIDLEY'S METHOD 444 CONCENTRATED-CHANGES TESTS 445 A
PAIRED-LINEAGES TEST 446 METHODS USING LIKELIHOOD * . 446 ADVANTAGES OF
THE LIKELIHOOD APPROACH 448 MOLECULAR APPLICATIONS 448 26 COALESCENT
TREES 450 KINGMAN'S COALESCENT 454 BUGS IN A BOX*AN ANALOGY 460 EFFECT
OF VARYING POPULATION SIZE 460 MIGRATION 461 XV EFFECT OF RECOMBINATION
464 COALESCENTS AND NATURAL SELECTION 467 NEUHAUSER AND KRONE'S METHOD
468 27 LIKELIHOOD CALCULATIONS ON COALESCENTS 470 THE BASIC EQUATION 470
USING ACCURATE GENEALOGIES*A REVERIE 471 TWO RANDOM SAMPLING METHODS 473
A METROPOLIS-HASTINGS METHOD 473 GRIFFITHS AND TAVARE'S METHOD . 476
BAYESIAN METHODS 482 MCMC FOR A VARIETY OF COALESCENT MODELS 482
SINGLE-TREE METHODS 484 SLATKIN AND MADDISON'S METHOD 484 FU'S METHOD
484 SUMMARY-STATISTIC METHODS 485 WATTERSON'S METHOD 485 OTHER
SUMMARY-STATISTIC METHODS 486 TESTING FOR RECOMBINATION 486 28
COALESCENTS AND SPECIES TREES 488 METHODS OF INFERRING THE SPECIES
PHYLOGENY 490 RECONCILED TREE PARSIMONY APPROACHES 492 LIKELIHOOD 493 29
ALIGNMENT, GENE FAMILIES, AND GENOMICS 496 ALIGNMENT 497 WHY PHYLOGENIES
ARE IMPORTANT 497 PARSIMONY METHOD 497 APPROXIMATIONS AND PROGRESSIVE
ALIGNMENT 500 PROBABILISTIC MODELS 502 BISHOP AND THOMPSON'S METHOD 502
THE MINIMUM MESSAGE LENGTH METHOD 502 THE TKF MODEL 503 MULTIBASE
INSERTIONS AND DELETIONS . C 506 TREEHMMS 507 TREES 507 INFERRING THE
ALIGNMENT 509 GENE FAMILIES 509 RECONCILED TREES 509 RECONSTRUCTING
DUPLICATIONS 511 ROOTING UNROOTED TREES 512 A LIKELIHOOD ANALYSIS 514
COMPARATIVE GENOMICS 515 XVI TANDEMLY REPEATED GENES 515 INVERSIONS 516
INVERSIONS IN TREES 516 INVERSIONS, TRANSPOSITIONS, AND TRANSLOCATIONS
516 BREAKPOINT AND NEIGHBOR-CODING APPROXIMATIONS 517 SYNTENY 517
PROBABILISTIC MODELS 518 GENOME SIGNATURE METHODS 519 30 CONSENSUS TREES
AND DISTANCES BETWEEN TREES 521 CONSENSUS TREES 521 STRICT CONSENSUS 521
MAJORITY-RULE CONSENSUS 523 ADAMS CONSENSUS TREE 524 A DISMAYING RESULT
525 CONSENSUS USING BRANCH LENGTHS 526 OTHER CONSENSUS TREE METHODS 526
CONSENSUS SUBTREES 528 DISTANCES BETWEEN TREES 528 THE SYMMETRIC
DIFFERENCE 528 THE QUARTETS DISTANCE 530 THE NEAREST-NEIGHBOR
INTERCHANGE DISTANCE 530 THE PATH-LENGTH-DIFFERENCE METRIC 531 DISTANCES
USING BRANCH LENGTHS 531 ARE THESE DISTANCES TRULY DISTANCES? 533
CONSENSUS TREES AND DISTANCES 534 TREES SIGNIFICANTLY THE SAME?
DIFFERENT? 534 WHAT DO CONSENSUS TREES AND TREE DISTANCES TELL US? 535
THE TOTAL EVIDENCE DEBATE 536 A MODEST PROPOSAL 537 31 BIOGEOGRAPHY,
HOSTS, AND PARASITES 539 COMPONENT COMPATIBILITY 540 BROOKS PARSIMONY
541 EVENT-BASED PARSIMONY METHODS 543 RELATION TO TREE RECONCILIATION
545 RANDOMIZATION TESTS 545 STATISTICAL INFERENCE 546 32 PHYLOGENIES AND
PALEONTOLOGY 547 STRATIGRAPHIC INDICES 548 STRATOPHENETICS 549
STRATOCLADISTICS 549 CONTROVERSIES 552 XVII A NOT-QUITE-LIKELIHOOD
METHOD 553 STRATOLIKELIHOOD 553 MAKING A FULL LIKELIHOOD METHOD 554 MORE
REALISTIC FOSSILIZATION MODELS 554 FOSSILS WITHIN SPECIES: SEQUENTIAL
SAMPLING 555 BETWEEN SPECIES 557 33 TESTS BASED ON TREE SHAPE 559 USING
THE TOPOLOGY ONLY 559 IMBALANCE AT THE ROOT 560 HARDING'S PROBABILITIES
OF TREE SHAPES 561 TESTS FROM SHAPES 562 MEASURES OF OVERALL ASYMMETRY
563 CHOOSING A POWERFUL TEST 564 TESTS USING TIMES 564 LINEAGE PLOTS 565
LIKELIHOOD FORMULAS 567 OTHER LIKELIHOOD APPROACHES 569 OTHER
STATISTICAL APPROACHES 569 A TIME TRANSFORMATION 570 CHARACTERS AND KEY
INNOVATIONS 571 WORK REMAINING 571 34 DRAWING TREES 573 ISSUES IN
DRAWING ROOTED TREES 574 PLACEMENT OF INTERIOR NODES 574 SHAPES OF
LINEAGES 576 UNROOTED TREES 578 THE EQUAL-ANGLE ALGORITHM 578 N-BODY
ALGORITHMS 580 THE EQUAL-DAYLIGHT ALGORITHM 582 CHALLENGES 584 35
PHYLOGENY SOFTWARE 585 TREES, RECORDS, AND POINTERS 585 DECLARING
RECORDS 586 TRAVERSING THE TREE 587 UNROOTED TREE DATA STRUCTURES 589
TREE FILE FORMATS 590 WIDELY USED PHYLOGENY PROGRAMS AND PACKAGES 591
REFERENCES 595 INDEX 644 |
| any_adam_object | 1 |
| author | Felsenstein, Joseph 1942- |
| author_GND | (DE-588)141921552 |
| author_facet | Felsenstein, Joseph 1942- |
| author_role | aut |
| author_sort | Felsenstein, Joseph 1942- |
| author_variant | j f jf |
| building | Verbundindex |
| bvnumber | BV017120349 |
| callnumber-first | Q - Science |
| callnumber-label | QH83 |
| callnumber-raw | QH83 |
| callnumber-search | QH83 |
| callnumber-sort | QH 283 |
| callnumber-subject | QH - Natural History and Biology |
| classification_rvk | WH 6000 |
| ctrlnum | (OCoLC)248886802 (DE-599)BVBBV017120349 |
| dewey-full | 581.38 578/.01/2 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 581 - Specific topics in natural history of plants 578 - Natural history of organisms |
| dewey-raw | 581.38 578/.01/2 |
| dewey-search | 581.38 578/.01/2 |
| dewey-sort | 3581.38 |
| dewey-tens | 580 - Plants 570 - Biology |
| discipline | Biologie |
| edition | 1. edition |
| format | Book |
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| id | DE-604.BV017120349 |
| illustrated | Illustrated |
| indexdate | 2024-07-20T07:52:08Z |
| institution | BVB |
| isbn | 9780878931774 0878931775 |
| language | English |
| lccn | 2003008942 |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-010321469 |
| oclc_num | 248886802 |
| open_access_boolean | |
| owner | DE-M38 DE-BY-UBM DE-634 DE-20 DE-11 DE-83 DE-188 DE-B16 DE-522 DE-Grf2 DE-29 |
| owner_facet | DE-M38 DE-BY-UBM DE-634 DE-20 DE-11 DE-83 DE-188 DE-B16 DE-522 DE-Grf2 DE-29 |
| physical | XX, 664 Seiten Illustrationen, Diagramme |
| publishDate | 2004 |
| publishDateSearch | 2004 |
| publishDateSort | 2004 |
| publisher | Sinauer |
| record_format | marc |
| spelling | Felsenstein, Joseph 1942- Verfasser (DE-588)141921552 aut Inferring phylogenies Joseph Felsenstein 1. edition Sunderland, Mass. Sinauer 2004 XX, 664 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Analyse cladistique - Mathématiques Análises cladística larpcal Botânica larpcal Filogenia larpcal Fylogenese gtt Wiskundige methoden gtt Árvores larpcal Mathematik Cladistic analysis Mathematics Mathematics Phylogeny Baum Mathematik (DE-588)4004849-4 gnd rswk-swf Phylogenie (DE-588)4076110-1 gnd rswk-swf Mathematisches Modell (DE-588)4114528-8 gnd rswk-swf Phylogenetische Systematik (DE-588)4174592-9 gnd rswk-swf Phylogenie (DE-588)4076110-1 s Phylogenetische Systematik (DE-588)4174592-9 s Baum Mathematik (DE-588)4004849-4 s Mathematisches Modell (DE-588)4114528-8 s DE-604 HEBIS Datenaustausch Darmstadt application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010321469&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Felsenstein, Joseph 1942- Inferring phylogenies Analyse cladistique - Mathématiques Análises cladística larpcal Botânica larpcal Filogenia larpcal Fylogenese gtt Wiskundige methoden gtt Árvores larpcal Mathematik Cladistic analysis Mathematics Mathematics Phylogeny Baum Mathematik (DE-588)4004849-4 gnd Phylogenie (DE-588)4076110-1 gnd Mathematisches Modell (DE-588)4114528-8 gnd Phylogenetische Systematik (DE-588)4174592-9 gnd |
| subject_GND | (DE-588)4004849-4 (DE-588)4076110-1 (DE-588)4114528-8 (DE-588)4174592-9 |
| title | Inferring phylogenies |
| title_auth | Inferring phylogenies |
| title_exact_search | Inferring phylogenies |
| title_full | Inferring phylogenies Joseph Felsenstein |
| title_fullStr | Inferring phylogenies Joseph Felsenstein |
| title_full_unstemmed | Inferring phylogenies Joseph Felsenstein |
| title_short | Inferring phylogenies |
| title_sort | inferring phylogenies |
| topic | Analyse cladistique - Mathématiques Análises cladística larpcal Botânica larpcal Filogenia larpcal Fylogenese gtt Wiskundige methoden gtt Árvores larpcal Mathematik Cladistic analysis Mathematics Mathematics Phylogeny Baum Mathematik (DE-588)4004849-4 gnd Phylogenie (DE-588)4076110-1 gnd Mathematisches Modell (DE-588)4114528-8 gnd Phylogenetische Systematik (DE-588)4174592-9 gnd |
| topic_facet | Analyse cladistique - Mathématiques Análises cladística Botânica Filogenia Fylogenese Wiskundige methoden Árvores Mathematik Cladistic analysis Mathematics Mathematics Phylogeny Baum Mathematik Phylogenie Mathematisches Modell Phylogenetische Systematik |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010321469&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT felsensteinjoseph inferringphylogenies |