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The Phylogenetic Handbook

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  • 57 b/w illus. 18 tables
  • Page extent: 750 pages
  • Size: 247 x 174 mm
  • Weight: 1.46 kg

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 (ISBN-13: 9780521730716)

The Phylogenetic Handbook
Cambridge University Press
9780521877107 - The Phylogenetic Handbook - A Practical Approach to Phylogenetic Analysis and Hypothesis Testing - Edited by Philippe Lemey, Marco Salemi and Anne-Mieke Vandamme
Index

Index

a posteriori trees 28

ABA multiple alignment program 81

abbreviations, amino acid 4

acceptance regions 378

accession numbers (AC) 36

adaptation of molecular sequences

See molecular adaptation

adaptive evolution 13

adaptive landscape models 13–14

ADAPTSITE software package 449

additive distance trees 148, 650, 655

adenine 4

affine gap penalties 73, 650

AIC criteria (Akaike Information Criteria) 234, 301, 427

definitions 650, 659

molecular clock analysis 371, 377

selecting models of evolution 345, 348, 349

Align-m multiple alignment program 81, 91

alignment 18, 45–47

AllAll multiple alignment program 81

alleles 8, 9, 11

allopatric speciation 15–16, 650, 661

AltAVisT web alignment comparison tool 103–104

alternative hypotheses 378

Amap multiple alignment program 81

amino acids 4, 575

ancestral recombination graph (ARG) 504, 650, 655

See also geneology

Anemonia sulcata (sea anemone) 154

aneuploidy 8

annotation 33

approximately unbiased (AU) test 388–389, 399, 400

ARG (ancestral recombination graph) 504, 650, 655

See also geneology

assumptions, implicit/explicit 341–342

asymptomatic normality 375, 431–432, 501, 650

AU (approximately unbiased) test 388–389, 399, 400

autapomorphy 650

autocorrelated relaxed clocks 367, 650

automated bootscanning 509

average-over-window-based scanning approaches 519, 521

background selection 558, 650

backtracking algorithms 46

bacteria 8, 490

balancing selection 10, 407, 592, 650, 655

BaliBase test case collection 89, 90, 92, 92–93

BaliPhy multiple alignment program 81

Base-by-Base multiple alignment editor 97

base trees 351

Bayes factor (BF) 233–235, 347, 439–440, 570

definition 651

Bayes, Thomas 211

Bayesian analysis 27, 210–216

burn-in 224

convergence 224–227

LAMARC 591

Markov Chain Monte Carlo sampling 220–224, 377, 560

Metropolis coupling 220, 227–229

mixing behavior 224–226

model choice/model averaging 232–235

phylogenetic inference 216–220, 636

phylogenetic models 230–232, 233–234

practice exercise

See MrBayes software

prior probability distributions 236

protein sequences 326

recombination detection 508

selection pressures on alignment 434

summarizing results 229–230

trace plot 224

Trypanosomatid phylogeny 334–338

See underBEAST software, Markov Chain Monte Carlo sampling

Bayesian Information Criteria

See BIC


BEAST (Bayesian evolutionary analysis by sampling trees) software 560–562, 572

amino acid sequences, translating data 575

analysis of output 579–582

Bayesian MCMC for geneology-base population genetics 562–565

burn-in 579, 584–585

computational performance 564–565

conclusions 571, 586–587

definitions/units 568

discussion 565–571

divergence time estimation 566–567

evolutionary models 560, 575

FigTree software program 586

input/output format 564

Markov Chain Monte Carlo 560, 577–578

maximum likelihood methodology 560

model comparison 568

molecular clock models 566

multiple data partitions 568

NEXUS file loading 573

parameters 568, 569–570

posterior probability limit 585

rate models among branches 566–567

relaxed molecular clock models 561

running analysis 578–579

setting dates of taxa 573–575

setting evolutionary model 575–576

setting MCMC options 578

setting operators 576–577

substitution models 566

trace plot 580, 581, 582, 583

tree priors 567

tree summarizing 582–585

TreeAnnotator tool 584

viewing annotated tree 585–586

web-based aids 587

BEAUti software package 568, 569–570, 572–578

BF

See Bayes factor

bias 313, 427, 611, 651

BIC (Bayesian Information Criteria) 234, 301, 347–349, 377, 651

definitions 651, 659

BioEdit multiple alignment editor 97

BIONJ 154

BLAST (Basic Local Alignment Search Tool) 33, 47–50, 52–54

database searching 62–66

definition 651

neighborhood word list 48

protein sequences 316, 317, 323–324, 331

Trypanosomatid phylogeny 335

BLAT database search tool 52

BLOSUM substitution matrices 45, 323, 331

definitions 651, 658

multiple sequence alignment 72, 73, 76, 88

bootscanning 198, 507, 509, 523, 524

bootstrap analysis 28

definitions 651, 656, 661, 663

detecting recombination 523, 524

maximum likelihood methodology 194

mtDNA data set 170–174, 175–176

pairwise distance methods 156, 157–159

parsimony analysis 268, 294

protein sequences 328

selection pressures on coding sequences 422

split networks 636, 640, 642–643

testing tree topologies 377, 382–383

bottlenecks, genetic 11, 493, 655

branch and bound technique 80, 90, 276–278, 651

branch-by-branch variation estimation 434, 466–471

branches, phylogenetic trees 20

branch-swapping 279

breakpoint detection 503, 508

Bremer support 295

See also decay index

Buneman index 630, 651, 656

Buneman tree 642, 643, 651

split networks 630–632, 635

burn-in 27, 336, 579, 584–585, 607

definitions 651, 653

centering 382

Chaos–Dialign multiple alignment program 81

character-based methods 326

character-state methodology 23–24

chimaeras, bacterial 490

cladograms 23, 164, 241, 456

definitions 651, 662

Clustal multiple alignment programs 81, 88–89, 93, 95

file formats/availability 100–101

protein sequences 321, 323, 326, 332

sequence data input format 62

TRIM5α gene sequence alignment 100–102

cluster analysis/clusters 20, 24–25, 144–148, 155

coalescent theory/coalescents 504, 547–548, 588, 651

advanced topics 557–559

coalescent-based inference 554–555

coalescent events 12

demographic history 552–554

effective population size 550–551, 651

Kingman coalescent 548–550

mutation clock 551–552

serial coalescent 555–557

Cobalt multiple alignment program 81, 94

codon

substitution models 420–422, 467

usage bias 313, 651

volatility 413–414, 651

coin tossing experiment 182

cold chains 227, 228, 651

compatibility matrix 507

compatibility methodology 502

complementary hydrogen-bonded pairs 4

confidence intervals 378, 431–434

confidence sets 390–391

conjugation 490, 651

See underrecombination

CONSEL software package 202, 393–394, 397–399, 400


consensus trees 294

See also supernetworks

consistency 422, 611, 651

consistency-based scoring 89, 651

constraint trees 296

contraAlign multiple alignment program 81

convergence 224–227

convergent evolution 19, 628, 651, 661

converse constraints 296

covarion/covariotide models 232

credibility intervals 229, 651, 653

credible sets 229, 653

criterion-based methods 267–268, 297–298

cytosine 4

DAD database 39

DAMBE software, assessing substitution saturation

invertebrateEF1a.FAS example 624–625

problem of substitution saturation 611–612

simian immunodeficiency genomes example 625–626

Steel’s method 612–617

vertebrate mitochondrial genomes example 620–624

Xia’s method 617–619

Darwin, Charles 13

databases 19, 33, 34, 106–108

BLAST searching 62–66

composite 39–44

ENTREZ 39, 41, 42–43, 55–57

errors 38

general nucleic acid sequence 35–37

general protein sequence 37–39

other tools 52–54

search strategies 33

searching by sequence similarity 45–54

sequence data input formats 59–62

specialized/secondary 39, 40–41

Datamonkey software package 450

dated tips, molecular clock analysis 363–364, 373–376

DCA (Divide and Conquer) program 82, 91

DDJB (DNA Data Bank of Japan) 19, 35, 320

DeBruijn dualization 635

decay index 295, 653

delete-half jackknifing 159

See also jackknifing

deletion errors 7

deoxyribonucleic acid

See DNA

deterministic evolution 12

deterministic forces 11

DiAlign multiple alignment programs 82, 91–92, 95

differences in sums of squares methodology 507

different rates (DR) models 363–364, 373–375

diploidy 9, 405, 547

definitions 653, 659, 666

directional selection 418, 492, 558, 592, 653

discrete character states 23

disruptive selection 16, 653

distance-matrix methodology 23, 24, 25, 508

See also genetic distances

divergence time 21–22

diversifying selection

See positive selection

Divide and Conquer (DCA) program 82, 91

DNA (deoxyribonucleic acid) 3–4

database of Japan (DDJ) 19

See also databases

vs. protein analysis 319–320

DNAML program 191–192

dN/dS ratio

definition 653

Influenza A case study 465–466, 469, 471, 476, 482

molecular adaptation 409, 411–413

and recombination 502

selection pressures on coding sequences 425–427

dot-matrix sequence comparison 74–75, 321–322

dynamic programming 46, 73, 273

definition 653

multiple sequence alignment 75–79

Edman degradation method 37

effective population size (EPS) 11

Bayesian evolutionary analysis 567

coalescent theory 550–551

definitions 651, 653, 659, 662, 666, 667

LAMARC 588, 589

molecular adaptation 409

molecular clock analysis 359

recombination detection 492

effective sample size (ESS) 226, 433, 579, 607

definitions 653, 659

efficiency 422, 611, 654

electrophoretic alleles 654

ELW (expected likelihood weights) 390–391, 396, 400

EMBL (European Molecular Biology Laboratory) 19, 35, 36, 38, 320

empirical Bayes approach 439, 654

enhancers 3

Ensembl database 40

ENTREZ databases 39, 41, 42–43, 55–57

EPS

See effective population size

ESS

See effective sample size

Essay Towards Solving a Problem in the Doctrine of Chances (Bayes) 211

EST (expressed sequence tag) databases 319

European Molecular Biology Laboratory (EMBL) 19, 35, 36, 38, 320

evolution

deterministic 12

fossil record 16

implications of recombination on 492–494

protein 311–320

units of 416

viruses 3, 8, 9

evolutionary

distances

See genetic distances

models

See model of evolution

networks 510, 627–629

rates 9–10, 157, 417, 654, 660

exhaustive searches 275


exons 8

expected likelihood weights (ELW) 390–391, 396, 400

exponential distributions 115

expressed sequence tags (EST) 37, 654

Expresso multiple alignment program 82, 93

extant taxa 20

external nodes, phylogenetic trees 20

extreme value distributions 49, 654

FastA software 33, 50–54, 323

database searching 66–67

definition 654

sequence data input format 59

FASTDNAML program 191–192

Felsenstein pruning algorithm 188, 189

finches, Galapagos Island 3, 13

FigTree software program 166–168, 586

fit index 635, 639–640, 654

Fitch algorithm 275

Fitch–Margoliash method 170, 171, 26, 326, 361

fitness 405, 415, 661, 654

survival of the fittest 13

fixation/fixation rates 9–10, 405, 654

fixed effects likelihood (FEL) models 438, 441–442, 474–477, 654

fluctuate (coalesce) function 594

fluctuating selection 407, 654

footprints, molecular 408–409

fossil record 16

founder effects 493

fourfold degenerate sites 7

four-point metric condition 148, 655

frequency-dependent selection 407, 655

G3PDH protein, model of evolution 357

GA

See genetic algorithms

Galapagos Island finches 3, 13

gap penalties/gap length penalties 45

gaps problem, multiple sequence alignment 72–74

GDE multiple alignment editor 97

GenBank 35, 36, 37, 58, 320

gene/s

database 42

duplication 8

frequencies 9

ontology (GO) 44

trees 21

Genedoc multiple alignment editor 97

geneology 16, 504, 547, 588

definitions 655, 659, 660

See also ancestral recombination graph (ARG)

geneology-based population genetics 561

general time reversible (GTR) models 121, 122, 174

generation times 10, 365, 556, 567, 604

definition 655

genetic algorithms (GA)

definition 655

maximum likelihood methodology 194

multiple sequence alignment 90–91

recombination detection 509

selection pressures on coding sequences 438

genetic bottlenecks 11, 493, 655

genetic code, universal 5, 6, 312–314

genetic distances 24, 111–112

choosing among different evolutionary models 140–141

definitions 651, 655, 658, 662

detecting recombination 500, 509, 521–524

estimating standard errors using MEGA4 135--137 131–132

impact on tree morphology 174–180

Jukes and Cantor models 117–118, 128–131

Kimura-parameters 3

Markov models 116–118

Markov process derivation 118–121

maximum likelihood estimators 113, 121

molecular clock analysis 358

nucleotide substitution models 112, 121–125

nucleotide substitution saturation 137–140

observed distance 112–113

Poisson process 113–116

protein sequences 319, 326

Q matrices 116, 117

rate heterogeneity 123–125, 133–135

selection pressures on coding sequences 422–425

software packages 126–128

split networks 630

substitution saturation 612

TN93 model 132–133

genetic drift 12, 310, 311, 551

definition 655

molecular sequences 403–404, 405

genetic exchange 8

See underrecombination

genetic hitchhiking (hitchhiking selection) 493, 558, 656

GenInfo (GI) number 37

Genious multiple alignment editor 97

genome 3

Genome Survey Sequences (GSS) 37, 655

GenPept database 39, 320–321

GI (GenInfo) number 37

global alignment 46

GO (gene ontology) 44

goodness-of-fit criterion 24, 267

graphical recombination detection 507

greedy stepwise addition 278, 279, 280

GSS (Genome Survey Sequences) 37, 655

GTR (general time reversible) models 121, 122, 174

guanine 4

HAMAP database 40

haploidy 405, 547, 567

definitions 655, 659, 666

Hastings ratio 655

HCV database 40

heated chains 227, 228, 651

heterologous (non-homologous) recombination 515, 660

heterotachy 611, 655


heterozygosity 9, 551, 655

heuristic strategies 24, 190, 506

hidden Markov models (HMMs) 72, 91, 655

hierarchical likelihood ratio tests (hLRTs) 343, 344–345, 346, 348

High Quality Automated and Manual Annotation of microbial Proteomes (HAMAP) database 40

highest posterior density (HPD) intervals 375, 579, 586, 653, 656

hill-climbing algorithms 284

hitchhiking selection 493, 558, 656

HIV data set 9, 40

drug resistance evolution 3

envelope gene example, model of evolution 356–357

likelihood mapping analysis 207

quartet puzzling consensus tree 202, 207–209

selection pressures on coding sequences 419

SplitsTree program 644–649

See underdetecting recombination

HIV sequences, detecting recombination 517–519

analysis of example sequence 529

detecting recombination 526–527

existing tools for recombination analysis 528

RDP3 534--542 542–544

SIMPLOT 529–532, 533–534

HLA database 41

hLRTs (hierarchical likelihood ratio tests) 343, 344–345, 346, 348

HMMs (hidden Markov models) 72, 91, 655

HOGENOM (Homologous sequences from complete Genomes) database 40

homogeneity 116, 656

homology/homologous

chromosomes 8

definition 656

genes 547

pairs 653

phylogeny/homology 17, 19

recombination 490, 515, 656

See underrecombination

sequence residues 68

See also multiple sequence alignment

sequences 33, 40, 314, 417, 650

sites 611

Homologous Vertebrate Genes (HOVERGEN) database 40

homoplasy 19, 269, 492, 507, 656

homozygosity 9

house-keeping proteins 310–311

HOVERGEN (Homologous Vertebrate Genes) database 40

HPD (highest posterior density) intervals 375, 579, 586, 653, 656

HTUs (hypothetical taxonomic units) 20

human histocompatibility locus A (IGMT/HLA) database 41

hydrophobicity/hydropathy profiles, protein 325

hyper-geometric random walks 509

hyperprior 214, 656

HyPhy analyses/software package

automating choices 483–484

codon model, fitting local 467

detecting recombination 463

estimating global rates 463–466

fixed effects likelihood 476

importing/manipulating sequence data files 456

Influenza A case study 451–452, 483–484

inspecting likelihood function 468

molecular clock analysis 370

previewing sequences 454

previewing trees 457

random effects likelihood methods 477–479

selection pressures on coding sequences 449

sequence alignment 458

summary of standard analyses 484–486

hypothetical taxonomic units (HTUs) 20

identifiers (ID) 35–36

IGMT/HLA database 41

Immunogenetics IMGT databases 41

indels 7, 73

infinite sites models 409, 492, 656

Influenza A case study 450–451, 486

α/β estimation 473

branch-by-branch variation estimation 466–471

comparison of internal and terminal branches 470–471

detecting recombination 461–463

dN/dS ratio estimation 465–466, 469, 471, 476, 482

estimating global rates 463–466

estimating nucleotide bases 460–461

estimating trees 458–460

fitting local codon model 467

fixed effects likelihood 474–477

gene-by-gene variation rate estimation 480

HyPhy analyses 451–452, 483–484

importing alignments and trees 452–453

inferring neighbor-joining tree/estimating branch lengths 460

inspecting likelihood function 468

interclade variation in substitution rates 469–470

nucleotide substitution models, comparison 462

preliminary analysis set-up 472

previewing sequences 453–455

previewing trees 455–457

random effects likelihood methods 477–479

reassortment 491

selection between different genes comparison 481–483

selection in different populations comparison 480–481

selection pressures between different clades 470

selection pressures on coding sequences 417–418

sequence alignments 457–458

simulations 484

single likelihood ancestor counting 473–474, 475, 476

site-by-site variation estimation 471–472

summary of standard analyses 484–486

UPGMA 458

See underHyPhy software package

information criteria 345–347

See also BIC

information entropy 612, 656

information releases, sequence databases 35

informative sites 502, 508, 661

ingroups 20

insertion errors 7

INTERALIGN multiple alignment program 82

internal nodes 20

internet searches 328–333

See also databases, web-based aids

introns 8, 318–319

invertebrateEF1a.FAS data set 624–625

IQPNNI software packages 192–193, 199–202, 203–207

IRMBASE test case collection 93

island model of migration 553, 656

isolation index 632, 651, 656, 664

iterative refinement methods 90

jackknifing 195, 268, 328, 377

definition 656

pairwise distance methods (p-distance) 156, 159

JalView multiple alignment editor 98

joint probabilities 219, 657

Jukes and Cantor (JC69) models 117–118, 128–131, 174

jumping of recombinant isolates 519, 520

jumping profiles 509

Kalign multiple alignment program 82

keyword searching 33, 44

Kimura-parameters (K80)/F84 genetic distances 3

Kingman coalescent 548–550

Kishino–Hasegawa (KH) test 384–385, 396, 399

Laboratoire d’ImmunoGénétique Moleculaire (IGMT/LIGM) 41

LAMARC software 588–589, 594, 595, 662

Bayesian vs likelihood sampling 591

conclusions 607–608

confidence intervals 604

converting data/file converter 600–601

definition 657

estimated parameter values 607

evolutionary model 592

fluctuate (coalesce) function 594

maximum likelihood estimators 590, 604

Metropolis–Hastings MCMC sampler 589–591

migrate-N function 594–595

multiple loci 598–599

output analysis 603–607

population parameters, estimating 601–603

population relative to sample size 593

practice exercise 599–600

program/package distinctions 596

random sample 591–592

rapid growth rates 599

recombine function 595–596

run time 593

sample size considerations 597–598

sequential samples 599

space and time 597

stability 592

starting values 596–597

trace plot 606–607

trees discarded 607

virus-specific issues 598

lateral gene transfer 8

lazy subtree rearrangement 193

least-squares fit 156

leaves 20

Leishmania mexicana enzyme analysis 328–333

likelihood 181, 269, 561

analysis 507

calculations 27

definitions 650–651, 657–658, 660, 664, 666

function 182, 212, 343, 421

mapping analysis 196–198, 207, 208

methodology 196–198, 207–208, 323, 590

scores 418

values 377, 663

See also maximum likelihood

likelihood ratio test (LRT) 194, 234, 301, 361, 605

definition 657

molecular clock analysis 361–363

and recombination 501, 510

selection pressures on coding sequences 429–430

statistic 380, 427, 657

testing tree topologies 380–382

lineage sorting 22, 23

linkage disequilibrium 491–492, 657

local alignment 46

local clock model 168, 365, 657

local-search methods 279

locus, genome 9

log odds matrices 45, 323, 658

long-branch attraction 27, 158, 269, 328, 611

definition 658

look-back time 314–316

LRT

See likelihood ratio test

MACAW multiple alignment program 82

MacClade multiple alignment editor 98

MAFFT multiple alignment program 82, 90, 95

majority rule concensus trees 230, 337, 564, 658

MAP multiple alignment program 83

marginal density 562

marginal probability distribution 218, 658

Markov Chain Monte Carlo (MCMC) sampling 27–28

Bayesian sampling 220–224, 377, 562–565

BEAST software 560, 577–578

definitions 651, 658, 659, 665, 666

geneology-base population genetics 562–565

LAMARC 589

maximum likelihood methods 193

molecular clock analysis 367, 375–376

protein sequences 334–338

selecting models of evolution 343

selection pressures on coding sequence alignments 434

testing tree topologies 380

Markov models 116–118, 174, 656, 658

Markov process 118–121, 420, 565, 655, 658

time-homogenous stationary 116, 118, 120, 140

mass spectrometry 37

Match-Box multiple alignment program 83

MAVID/AMAP multiple alignment program 83

MAXCHI substitution distribution method 525, 536

maximum chi-squared test 506

maximum likelihood 183, 333, 622, 658, 663

maximum likelihood estimators (MLEs) 183

BEAST software 560

coalescent theory 554

definitions 658, 662

distance methods 142

genetic 113, 121

LAMARC software 590, 604

molecular clock analysis 375, 376

mtDNA data set 185

selecting models of evolution 343

maximum likelihood methodology 24, 25, 27, 181–184

assumptions 341

BEAST software 560

branch support 194–195, 203–207

complex case 185–186

computing probability of alignment for fixed tree 186–187

distance methodology 154

DNAML/FASTDNAML 191–192

Felsenstein pruning algorithm 188, 189

finding maximum-likelihood tree 189–190

full-tree rearrangement 190–191

genetic algorithms (GA) 194

heuristic strategies 190

IQPNNI 192–193, 199–202, 203–207

likelihood mapping analysis 196–198, 207

ML tree construction example 199–202

molecular clock analysis 361

Mr Bayes software 234

parameter estimation 195

PAUP* program 267, 300–309

PHYML/PHYML-SPR 192

protein sequences 323, 326

quartet puzzling 195–196, 203–209

RAxML 193

selection pressures on coding sequences 416, 424–425

simple case: two sequences 184–185

simulated annealing 193

software packages 199

split networks 636

testing tree topologies 377

maximum parsinomy (MP) 26–27, 142, 187, 326, 636

definitions 653, 658

McDonald–Kreitman test 413, 658–659

MCMC

See Markov Chain Monte Carlo (MCMC) sampling

MCMCMC

See Metropolis coupling

ME

See minimum evolution

measurably evolving populations (MEPs) 363, 555, 659

median networks 629, 634, 636

MEDLINE 42

MEGA sequence data input format 61–62

MEGA4 software package 160, 161

genetic distances 135–137, 174–180

selection pressures on coding sequences 449

meiosis 8, 490, 659

See underrecombination

MEPs (measurably evolving populations) 363, 555, 659

Metropolis coupling (MCMCMC) 220, 227–229, 651, 659

Metropolis–Hastings (MCMC) sampling 220, 560–561, 589–591

definitions 655, 657, 659

microsatellites 598, 659

midpoint rooting 21, 166, 361, 659

migrate-N function 594–595

migration/migration rates 15, 553, 588, 657, 659

minimum evolution (ME) 149, 268, 613

definitions 658, 659, 660

mixing behavior 224–226, 581

definitions 653, 659, 666

MLEs

See maximum likelihood estimators

MMDB (Molecular Modeling Database) 42

model averaging 349–350, 659

models of evolution 24, 341–342

Bayesian approaches 347–348

BEAST software 560

coalescents 554

definitions 655, 660

G3PDH protein example 357

genetic distance approaches 140–141, 142

hierarchical likelihood ratio tests 343, 344–345, 346, 348

HIV-1 envelope gene example 356–357

information criteria 345–347

LAMARC software 592

model averaging 349–350

model fit 342–343

model selection procedure 351

model selection uncertainty 348–349

MODELTEST program 351–354, 355

PAUP* 352, 353, 351

performance-based selection 348

PROTTEST 354–355, 357

selection pressures on coding sequences 416, 428

substitution models 217, 316, 656, 660, 666

testing tree topologies 377

vertebrate mtDNA model selection example 355–356

model of (sequence/molecular) evolution 181, 590, 660

MODELTEST program 351–354, 355, 377

modified Sherman test 507

molecular adaptation 403, 414

balancing selection 407

basic concepts 403–407

codon volatility 413–414

comparative methods 409

fixation 405

genetic drift 403–404, 405

molecular footprint of selection 408–409

mutations 403, 404

positive selection 405, 405

summary statistic methods 409, 409–411

See also molecular evolution

molecular clock analysis 23, 358–359, 367–368

BEAST software 561

coalescent 551

dated tips 363–364, 373–376

definitions 657, 660, 666

Fitch–Margoliash method 361

genetic distances 111, 144

likelihood ratio test 361–363

Markov Chain Monte Carlo 363, 375–376

maximum likelihood estimators/methodology 361, 375, 376

NEWICK sequence data input format 372–373

PAML 369–371, 373

PAUP* 370

proteins 359

and recombination 501

relative rate test 360–361

selecting models of evolution 342

TREE-PUZZLE software package 370

TRIM5α gene sequence alignment 369–373

viral sequence analysis, RSVA data set 373–376

See also relaxed molecular clock models

molecular evolution

data, phylogenetic 16–19

databases 19

genetic information 3–8

multifurcating trees 28–29

phylogenetic trees 19–23, 23–28

population dynamics 9–14

rates 561, 663, 666

speciation 14–16

terminology 9–10, 16, 20

See also molecular adaptation

molecular footprints 408–409

Molecular Modeling Database (MMDB) 42

monophyletic taxa 20, 154, 292, 564

definitions 651, 657, 660

Monte Carlo simulation 345, 363, 383, 502

definitions 660, 661

See underMarkov Chain Monte Carlo sampling

MP

See maximum parsinomy

MrBayes software 237

acquiring/installing software 237

analysis based on primates data file 240

analyzing partitioned data set 261–266

changing the window size 238–239

checking model 247–248

data entry 241–242

data partitioning 261–263

entering mixed data 261

getting started 238

help command 239

maximum likelihood analysis 234

model specification 242–244

quick start version 240–241

running analysis 252–254, 265

setting priors 244–247

setting up analysis 248–252

specifying partitioned model 263–265

stopping analysis 254–255

summarizing samples of substitution model parameters 255–257

summarizing samples of trees and branch lengths 257–261

useful tips 265–266

MSA multiple alignment program 83

mtDNA data set 72, 73, 76, 88

bootstrap analysis 170–174, 175–176

Fitch–Margoliash method 170, 171

maximum likelihood estimators 185

models of evolution 355–356

SplitsTree program 638–644

substitution saturation, assessing with DAMBE software 620–624

Multalin multiple alignment program 83

multifurcating trees, molecular evolution 28–29

Multi-Lagan multiple alignment program 83

multi-model inference (model averaging) 349–350, 659

multiple sequence alignment 68, 69, 87

algorithms/programs 79–80, 81–86, 87–92

BaliBase test case collection 89, 90, 92, 92–93

BLOSUM matrix 62

choosing a program 93–95

consistency-based scoring 89

dot-matrix sequence comparison 74–75

dynamic programming 75–79

gaps problem 72–74

hidden Markov models software 72, 91

iterative refinement methods 90

multiple alignment algorithms/programs 79–80, 81–86, 87–92

nucleotide sequences vs. amino acid sequences 95–96

pairwise sequence alignment 74–79

PAM matrix 72, 88

practice exercise

See TRIM5α gene sequence alignment

progressive alignment 80, 87, 87–89

protein sequences 323–324

repeats problem 68–70

substitutions problem 70–72

T-COFFEE multiple alignment program 86, 89–90

testing multiple alignment methods 92–93

visualizing alignments/manual editing 96–100

MUMMALS multiple alignment program 83, 91

Murlet multiple alignment program 83

MUSCA multiple alignment program 83

MUSCLE multiple alignment program 84, 90, 95, 102

mutation clock 551–552

See undermolecular clocks

mutations 6–8, 12, 13, 403, 404

synonymous/non-synonymous 7, 10–12, 133, 408, 502

See also dN/dS ratio

transition/transversion 7, 666

mutation rates 9–10, 551, 589

definitions 659, 660, 666, 667

National Centre for Biotechnology Information (NCBI) 19, 40

National Library of Medicine (NLM) 19

natural selection 12

See also molecular adaptation

NCBI (National Centre for Biotechnology Information) 19

NCBI Map Viewer 40

nearest neighbor interchange (NNI) 191, 281, 660

negative selection 310, 405, 415, 558, 660

neighbor-joining (NJ) methodology 26, 361

definitions 660, 662, 665

detecting recombination 523, 524

HIV data set 645

multiple sequence alignment 87

pairwise distance methods 149–154, 155, 163–168, 178–179

selection pressures on coding sequences 420

split networks 631

neighbor similarity scores 507

NeighborNet algorithm 629, 635–636, 645, 647–649

networks 628

See also split networks

neutral theory of molecular evolution 13

NEWICK sequence data input format 161, 162, 167, 332, 372–373

NEXUS sequence data input format 59, 161, 352

BEAST software 573

Mr Bayes software 257–8

parsimony-based inference 287, 300

Trypanosomatid phylogeny 335–336

NJ

See underneighbor-joining methodology

NLM (National Library of Medicine) 19

NMR (nuclear magnetic resonance) 38

nodes 20

non-degenerate sites 7

non-homologous recombination 515, 660

non-parametric bootstrap

See bootstrap analysis

non-sense codes 5

non-synonymous mutations 415

non-synonymous/synonymous rate ratio

See dN/dS ratio

non-synonymous substitutions 316, 660

nuclear magnetic resonance (NMR) 38

Nucleotide database 42

nucleotide sequences 4, 95–96

nucleotide substitution models 174, 361

bias correction 427

genetic distances 112, 121–125

Influenza A case study 462

Markov process 174

TRIM5α gene sequence alignment 136

See also model of evolution

nucleotide substitution saturation

See substitution saturation

nuisance parameters 28, 343, 555, 562

definitions 660, 662

null hypothesis 378

objective function 267

observed distance 112–113

See also pairwise distance methods

one-sided Kishino–Hasegawa test 385–386, 396, 399

Online Mendelian Inheritance in Man (OMIM) 42

ontology 661

open reading frames (ORFs) 6, 7–8

operational taxonomic units (OTUs) 20

optimal alignment 46

optimality

criteria 24, 267

principle 75, 77–78

ORALGEN database 40

ORFs (open reading frames) 6, 7–8

orthologous

genes 19, 661

proteins 310

sequences 665

OTUs (operational taxonomic units) 20

outer planar networks 634

outgroup/s 147, 360, 661

routing 20, 21, 168–170, 327

sequences 410

taxa 292

overdominance 407, 661

OXBENCH test case collection 93

pairwise distance methods (p-distance) 142–144, 159–160

bootstrap analysis 156, 157–159, 170–174, 175–176

cluster analysis (UPGMA/WPGMA) 144–148, 155

definition 661

editing phylogenetic trees 167

Fitch–Margoliash method 170, 171

genetic distances, impact on tree morphology 174–180

jackknifing 156, 159

minimum evolution 149

neighbor-joining methodology 149–154, 155, 163–168, 178–179

outgroup routing 168–170

PHYLIP software package 160–163, 170–174

programs to display/manipulate phylogenetic trees 161–162

pairwise homoplasy index 509

pairwise sequence alignment 74–79

PAM (point-accepted mutation) 661

substitution matrices 45, 72, 88, 658

protein sequences 316–318

PAML (Phylogenetic Analysis by Maximum Likelihood) 369–371, 373, 448

panmictic populations 548, 661

parallel evolution 19, 628, 651, 661

paralogous

genes 19, 661

isoenzymes 327

parametric bootstrap

See Monte Carlo simulation

See also Markov Chain Monte Carlo (MCMC) sampling

parapatric speciation 16, 661

paraphyletic taxa 20, 661

see also parsimony analysis maximum parsinomy 267–268, 278, 612

approximate methods 279–285

background 268–270

branch and bound technique 276–278

calculating length of given tree 270–273

exact methods 275–279

Fitch’s algorithm 275

generation of all possible trees 276

hill-climbing algorithms 284

implicit assumptions 341

length 26–27

nearest neighbor interchange (NNI) 281

practice exercise

See underPAUP*

Sankoff’s algorithm 274

searching for optimal trees 273

stepwise addition 278, 279, 280

subtree pruning and regrafting 281, 282, 283

tree bisection and reconnection 282–283

parsimony informative sites 502, 508, 661

partition matrices 507

pathogenicity in bacteria 490

patristic distance 156, 661

PAUP* program 160, 180, 286–289, 326

analyzing data through command–line interface 289

commands/options 288–289

distance optimality criteria 297–300

maximum likelihood methodology 267, 300–309

models of evolution 351, 352, 353

molecular clock analysis 370, 372

parsimony analysis/tree searching 290–297

running the program 287–288

PCMA multiple alignment program 84

PDB (Protein Data Bank) 41

phenetic distances 630, 662

phenograms 144, 662

PHYLIP software package 126–128, 160–163, 170–174, 371

Phylogenetic Analysis by Maximum Likelihood

See underPAML

phylogenetic compatibility methodology 509

phylogenetic hidden Markov model 508

phylogenetic trees 183

Phylogeny Inference Package (PHYLIP) 126–128, 160–163, 170–174, 371

phylograms 23, 164, 241, 292, 456

definitions 651, 662

PhyML software package 192, 332

PileUp multiple alignment program 84

PIMA multiple alignment program 84

POA multiple alignment program 84, 95

point-accepted mutation

See PAM

point mutations 6

Poisson process 113–116, 174

polymorphisms 9, 404

polynucleotide structure 3–4

polyploidy 8

polytomies 29, 209, 292, 644, 662

PopSet database 42

population dynamics 9–14

population mutation rate 504, 660

See also theta

population recombination rates 490, 503–505, 557, 588

definitions 657, 662

positional homology 18

positive selection 310, 359, 415, 419, 492

definitions 651, 653, 662

molecular sequences 405, 405

and recombination 501

posterior 659

posterior probability distribution 27, 347

Bayesian evolution by sampling trees 561

definitions 659, 662

maximum likelihood methodology 195

molecular clock analysis 347

MrBayes software 215

protein sequences 328

selection pressures on alignments 434

Trypanosomatid phylogeny 334

posterior probability limit 585

potential scale reduction factor (PSRF) 226, 662

Praline multiple alignment program 84, 94

PREFAB test case collection 93

PRF (Protein Resource Foundation) 39

primates data set 163–168, 240

PRIME multiple alignment program 84

prior probability distributions 27

Bayesian phylogenetic analysis 212, 236, 347, 434

definition 651, 656, 662

molecular clock analysis 367

priors, vague/uninformative 217

probabilistic divergence methodology 508

probability density function 213, 549, 662

probability mass function 212, 213, 662

Probalign multiple alignment program 84

ProbCions multiple alignment program 84, 93, 95

ProDa multiple alignment program 85, 92


profile likelihood 432, 433, 605, 662

progressive alignment 80, 87–89, 662

Promals multiple alignment program 85, 94

promotors 3

PROSITE protein motif database 94

PROTAL2DNA alignment tool 104–105

Protdist program 326

Protein Data Bank (PDB) 41

Protein database 42

protein identifiers 37

protein sequences in phylogenetic analysis 310–311

alignment of two-protein sequences 321–323

analyzing protein sequences 311

codon usage bias 313

DNA or protein choice 319–320

dot-matrix sequence comparison 321–322

evolutionary distance, and protein differences 319

genetic code, universal 312–314

inferring protein phylogeny 326–327

introns/non-coding DNA 318–319

Leishmania mexicana enzyme analysis 328–333

look-back time 314–316

majority rule concensus tree 337

manual adjustment of protein alignments 324–325

Markov Chain Monte Carlo 334–338

maximum likelihood tree, Leishmania mexicana 333

molecular clock analysis 359

multiple sequence alignment 323–324

phylogenetic trees construction 320–328

protein evolution 311–320

protein/nucleic acid search comparison 317

reliability of inferred trees 328

retrieval of protein sequences 320–321

rooting a tree 327

sequence divergence in proteins 316–318

tree building 326–328

Trypanosomatid phylogeny 334–338

Protein Resource Foundation (PRF) 39

protein synthesis 3

PROTTEST 354–355, 357

PRRN/PRRP multiple alignment program 85, 90

PSAlign multiple alignment program 85

PSI-BLAST 94

See also BLAST

PSRF (potential scale reduction factor) 226, 662

PubMed database 42

purifying selection 310, 405, 415, 558, 660

purines 4

puzzle support values 196

See also quartet puzzling

pyrimidenes 4

Q matrices 116, 117, 231, 361, 662–663

QOMA multiple alignment program 85

quartet puzzling 126, 300, 377

definition 663

HIV data set 202, 207–209

maximum likelihood methodology 195–196, 203–209

quartet scanning 509

quasispecies 9, 663

QuickJoin 154

random effects likelihood (REL) methods

definitions 654, 663

HyPhy software package 477–479

Influenza A case study 477–479

selection pressures on coding sequences 438–440

rate/s

growth or decline 552

heterogeneity 123–125, 133–135

RAxML 193

RDP3 software program 508

exploratory analysis 534–542

HIV sequences, detecting recombination 534–544

refining recombination hypothesis 542–544

tree reconstruction 541

reading frames, genetic 5

reassortment 491, 515, 663

See underrecombination

recombination analysis 8, 29, 488, 502, 509, 515–516

average-over-window-based scanning approaches 519, 521

breakpoint detection 503

detecting 502, 516–519, 526–527

See also HIV sequences

detecting recombination, requirements 516–519

evolutionary implications 492–494

genetic distances 500, 509, 521–524

jumping of recombinant isolates 519, 520

linkage disequilibrium 491–492

mechanisms of recombination 488–491

molecular clocks 501

Monte Carlo simulation 502

neighbor-joining methodology 523

overview of detection tools 505–513

parametric bootstrap 502

performance of recombination detection tools 513–514

phylogenetic inference, impact on 494–502

positive selection 501

rate variation among lineages 500–501

rate variation among sites 500

rates

See population recombination rates

signals, recombination 519

similarity/dissimilarity methods 522

software tools 517, 523–525, 528

substitution distribution methods 523, 525

substitution patterns 492, 493

theory 519–526

tree shapes/branch lengths 488

Refina multiple alignment program 85

RefSeq database 40

relative rate test 360–361, 663


relaxed molecular clock models 23, 365–367, 375

Bayesian analysis 230–231

BEAST 561

coalescent 558

definition 663

distance methodology 168

RELL (resampling estimated log likelihoods) 382–383, 663

repeats problem, multiple sequence alignment 68–70

replacement/non-synonymous mutations 408

reproductive isolation 15

resampling estimated log likelihoods (RELL) 382–383, 663

restriction fragment length polymorphisms (RFLPs) 16

reticulation networks 629

reversible-jump MCMC 235, 347, 570, 651, 664

RFLPs (restriction fragment length polymorphisms) 16

RNA (ribonucleic acid) 3

rooted phylogenetic trees 20, 21

RSVA data set 373–376

SAGA multiple alignment program 85

Salmonella data set 644–649

SAM multiple alignment program 85

sampling distributions 378, 664

sampling importance resampling (SIR) algorithm 432, 664

sampling variance 664

Sankoff’s algorithm 274

SATCHMO multiple alignment program 86, 91

saturation

See substitution saturation

Sawyer’s statistical test for gene conversion 506

s-coalescent 664

Se-Al multiple alignment editor 98

SeaView multiple alignment editor 98

segregating sites 410, 492, 664

selection coefficients 405, 664

selection pressures on coding sequences 415–416, 446–447

asymptomatic normality 431–432

Bayesian approaches 434

bootstrap analysis 422

branch-by-branch variation estimation 434

codon substitution models 420–422

comparison of rate distributions in different genes 441

confidence intervals 431–434

data driven branch specification 436–438

distance-based approaches 422–424

dN/dS estimation 425–427

evolutionary models, choosing among different 428

fixed effects likelihood models 438, 441–442

HIV example 419

hypothesis testing 427–431

influenza example 417–418

likelihood ratio test 429–430

local vs. global model 435

maximum likelihood methodology 416, 424–425

MEGA4 software package 449

method choice 443

neighbor-joining methodology 420

neutral situations 416–417

nucleotide substitution bias correction 427

phylogenies, effect of 417–418

practice exercises

See Influenza A case study

prerequisites 419–420

a priori specification 435–436

profile likelihood 432, 433

random effects likelihood models 438–440

rate comparison in different branches 445–446

sampling techniques 432–434

selection types 418–419

simulated data 422

single likelihood ancestor counting methods 442–443, 444

software packages 448–450

synonymous rate variation 445

units of evolution 416

selective pressure, positive/negative 10

selective sweeps 419, 493, 558, 653, 664

sense codes 5

SEQDB 39

sequence databases

See databases

sequence divergence in proteins 316–318

See also PAM

sequence identifiers 33

Sequence Retrieval System (SRS) 43–44

sequence version archive 36–37

serial coalescent 555–557, 664

Shannon’s entropy (information entropy) 612, 656

Shimodaira-Hasegawa (SH) test 386, 387, 399

sickle-cell anemia 10

signals, recombination 519

silent mutations 408

simian immunodeficiency (SIV) genomes data set 625–626

similarity 17–18, 33, 45, 93, 522

SIMPLOT software package 524, 528, 529–532

detecting recombination 529–534

mapping recombination 532, 533

SIMPLOT groups feature 533–534

simulated annealing 193, 664

single likelihood ancestor counting (SLAC) 383

Influenza A case study 473–474, 475, 476

selection pressures on coding sequences 442–443, 444

single nucleotide polymorphisms (SNPs) 664

single rate dated tip (SRDT) models 363–364, 373–375

SIR (sampling importance resampling) algorithm 432, 664

sister scanning methodology 508

sister taxa 168, 613, 658, 664

site-frequency 408, 664

SLAC

See single likelihood ancestor counting

SNPs (single nucleotide polymorphisms) 664


software packages

genetic/evolutionary distances 126–128

maximum likelihood methodology 199

recombination events 517, 523–525, 528

selection pressures on coding sequences 448–450

testing tree topologies 393

SOWH (Swofford-Olsen-Waddell Hillis) test 389–390

spatial phylogenetic variation 507

speciation 14–16

species trees 21

spectral analysis 633

SPEM multiple alignment program 86, 94

splicing 8

split decomposition 198, 632–634, 629

definitions 654, 664

HIV data set 645

Salmonella data set 646

split networks 654, 656

Buneman tree 630–632, 635

consensus/supernetworks 629, 636–637

definition 664

evolutionary relationships as networks 627–629

median networks 629, 634, 636

NeighborNet algorithm 629, 635–636, 645, 647–649

origin/introduction of term 629

outer planar networks 634

practice exercise

See SplitsTree program

split decomposition 632–634

theory 629–630

weakly compatible splits to networks 634–635

weighted networks 632, 635

weighted trees 629

splits 651, 656, 664

SplitsTree program 638, 640

bootstrap analysis 640, 642–643

Buneman tree 642, 643

computing different networks 642

computing trees 642, 643

downloading 638

fit index 635, 639–640

getting started 639

HIV data set 644–649

laying out split networks 641

mtDNA data set, using on 638–644

NeighborNet algorithm 647–649

printing 643–644

recomputing split networks 641–642

Salmonella data set 644–649

split decomposition tree 646

SPR (subtree pruning and regrafting) 191, 223, 281, 665

SRDT (single rate dated tip) models 363–364, 373–375

SRS (Sequence Retrieval System) 43–44

SSAHA database search tool 52

star decomposition 190, 459, 660, 664–665

star-like radiation 209

stationarity 116, 187, 222, 420, 611

definitions 665, 666

statistical parsimony networks 629

Steel’s method 612–617

stepping-stone model of migration 553, 665

stepwise addition 190, 278, 665

stepwise recombination detection 509

stochastic

evolution 12, 13

forces 11

strictly bifurcating trees 28

substitution distribution methodology 502, 523, 525

substitution models 217, 316, 656, 660, 666

See also models of evolution

substitution patterns, recombination 492, 493

substitution rates 9–10, 420, 566

substitution saturation 113, 137–140, 315

definition 665

problem of 70–72, 611–612

See also DAMBE software

sub-tree pruning and regrafting (SPR) 191, 223, 281, 665

summary statistic methods 409, 409–411

supernetworks 629, 636–637

survival of the fittest 13

SwissProt 316, 320, 325

Leishmania mexicana enzyme analysis 329–331

Uniprot knowledgebase 38

Swofford–Olsen–Waddell Hillis (SOWH) test 389–390

symmetrical/non-symmetrical recombination 490

sympatric speciation 16, 665

synapomorphy 612, 665

synonymous rate variation 445

synonymous substitutions 665

synonymous/non-synonymous mutations 7, 10–12, 133, 408, 502

See also dN/dS ratio

Taijma’s D summary statistic 410, 665

Taxonomy database 42–43

TBR (tree bisection and reconnection) 191, 282–283, 666

T-COFFEE multiple alignment program 86, 89–90, 93, 95, 102

testing tree topologies 377–378, 383, 391–392

approximately unbiased test 388–389, 399, 400

confidence sets 390–391

CONSEL software package 202, 393–394, 397–399, 400

definitions, distributions and testing 378–380

expected likelihood weights 390–391, 396, 400

Kishino–Hasegawa test 384–385, 399

likelihood ratio distribution 381–382

likelihood ratio test 380–381

non-parametric bootstrap 382–383

one-sided Kishino-Hasegawa test 385–386, 396

Shimodaira–Hasegawa (SH) test 386, 387, 399

software packages 393

Swofford–Olsen–Waddell Hillis (SOWH) test 389–390

tree tests, general structure 384

TREE-PUZZLE 393–394, 394–397, 399, 400

weighted test variants 386–388, 399

theta 665–667

third party annotations (TPA) 37

thymine 4

time to the most recent common ancestor (TMRCA) 21

time-homogenous stationary Markov processes 116, 118, 120, 140

TN93 model 132–133

topology, tree 20

TPA (third party annotations) 37

trace plot

BEAST software 580, 581, 582, 583

definition 666

LAMARC software 606

Bayesian phylogenetic analysis 224

traceback 77–78

Tracker/Anchored Dialign multiple alignment program 86

transduction 490, 666

See underrecombination

transformation 490, 666

See underrecombination

transition mutations 7, 666

See also transversion/transition ratios

transversion 666

models 356–357

mutations 7

See also transversion/transition ratios

transversion/transition ratios

Bayesian analysis 565

database searching 45

definition 666

distance methodology 122, 131–132, 163

LAMARC 602

maximum likelihood methodology 183

recombination detection 532

selecting models of evolution 342

selection pressures on alignments 417

substitution saturation 612

TreeAnnotator tool 584

tree bisection and reconnection (TBR) 191, 282–283, 666

TREECON 160

TreeEdit algorithm 372

TREE-PUZZLE software package

distance methodology 126–128, 132–133, 140–141, 161

likelihood mapping analysis 208

maximum likelihood methodology 195, 203–207

molecular clock analysis 370

parsimony 300

protein sequences 326

testing tree topologies 393–397, 399, 400

TreeView algorithm 164–166, 168, 172–173, 372, 528

TrEMBL 38

TRIM5α gene sequence alignment 100–108

ClustalW multiple alignment program 100–102, 103–104

comparison of alignments 103–104

databases of alignments 106–108

editing/viewing alignments 105–106

Jukes and Cantor (JC69) models 128–131

molecular clock analysis 369–371, 371–373

MUSCLE multiple alignment program 102, 104

neighbor-joining (NJ) methodology 163–168, 178–179

nucleotide substitution models 136

protein to nucleotide alignment 104–105

T-COFFEE multiple alignment program 102

Trypanosoma brucei 325

Trypanosoma congolense 313

Trypanosomatid phylogeny 313, 334–338

twofold degenerate sites 7

UCSC Genome Browser 40

ultrametric/ultrametricity

definitions 660, 666

ultrametric trees 144, 147–9, 155, 361, 500

unorrelated relaxed clocks 367, 566, 666

UniGene database 40, 42

uninformative priors 217

Uniprot knowledgebase 38, 316, 320–321, 324

Uniprot splice variants 38

UniRef100/90/50 38

units of evolution 416

unrooted models 20, 148, 230, 361

definitions 657, 666

UPGMA (unweighted pair group method with arithmetic means) 26

definitions 666–667

genetic distances 140

Influenza A case study 458

molecular clock analysis 361

pairwise distance methods 144–148, 155

parsimony analysis 268

protein sequences 326

split networks 631

uracil 4

vague/uninformative priors 217

version number 36–37

vertebrate mtDNA data set

See mtDNA data set

viruses

evolution 3, 8, 9, 16

genetic exchange 490–491, 515–516

See underrecombination

LAMARC software 598

molecular clock analysis 373–376

visual recombination detection 509

Watterson estimate 596, 667

web-based aids 587

weighbor 154

weighted

neighbor-joining 154

networks 632, 635

test variants 386–388, 399

trees 629

weighted-pair group method with arithmetic means (WPGMA) 144–148

whole genome shotgun (WGS) sequences 37

wild-type genotype 403

wobble position 312, 314–315

WPGMA (weighted-pair group method with arithmetic means) 144–148

Wright–Fisher population model 548, 550, 653, 667

WSP objective functions 79–80, 90, 91

Xia’s method, substitution saturation 617–619

X-ray crystallography 38




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