The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis TestingMarco Salemi, Anne-Mieke Vandamme, Philippe Lemey The Phylogenetic Handbook is a broad, hands on guide to theory and practice of nucleotide and protein phylogenetic analysis. This second edition includes six new chapters, covering topics such as Bayesian inference, tree topology testing and the impact of recombination on phylogenies, as well as a detailed section on molecular adaptation. The book has a stronger focus on hypothesis testing than the previous edition, with more extensive discussions on recombination analysis, detecting molecular adaptation and genealogy-based population genetics. Many chapters include elaborate practical sections, which have been updated to introduce the reader to the most recent versions of sequence analysis and phylogeny software, including BLAST, FastA, Clustal, T-coffee, Muscle, DAMBE, Tree-puzzle, Phylip, MEGA, PAUP*, IQPNNI, CONSEL, ModelTest, Prottest, PAML, HYPHY, MrBayes, BEAST, LAMARC, SplitsTree, and RDP. Many analysis tools are described by their original authors, resulting in clear explanations that constitute an ideal teaching guide for advanced-level undergraduate and graduate students. |
Contents
Sequence databases and database searching | 33 |
Practice | 55 |
Multiple sequence alignment | 68 |
Practice | 100 |
Genetic distances and nucleotide substitution models | 111 |
Practice | 126 |
Phylogenetic inference based on distance methods | 142 |
Practice | 161 |
Natural selection and adaptation of molecular sequences | 407 |
Estimating selection pressures on alignments of coding sequences | 419 |
Practice | 452 |
Recombination | 493 |
Detecting and characterizing individual recombination events | 519 |
Practice | 532 |
population genetic inference using genealogies | 551 |
Bayesian evolutionary analysis by sampling trees | 564 |
Phylogenetic inference using maximum likelihood methods | 181 |
Bayesian phylogenetic analysis using MRBAYES | 210 |
Practice | 237 |
Phylogeny inference based on parsimony and other methods | 267 |
Practice | 289 |
Phylogenetic analysis using protein sequences | 313 |
Selecting models of evolution | 345 |
Practice | 355 |
H Molecular clock analysis | 362 |
Practice | 373 |
Testing tree topologies | 381 |
Practice | 397 |
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Common terms and phrases
algorithm amino acid ancestor Bayesian Biology bootstrap branch lengths chain Chapter clade CLUSTAL cluster coalescent codon codon position computed confidence data set database default defined detection difficult distribution dN/ds evolution example file find first fit fixed format frequencies gene genealogy genetic distances genome HYPHY hypothesis inference input Kosakovsky Pond LAMARC likelihood function lineages Markov matrix maximum likelihood MCMC menu methods model parameters molecular clock MRBAYES multiple alignment multiple sequence alignment mutation neighbor-joining NEXUS node nucleotide nucleotide substitution obtained optimal option OTUs outgroup output pairwise parsimony partition PAUP PHYLIP phylogenetic analysis phylogenetic trees phylogeny population positive selection posterior probability protein sequences quartet rate heterogeneity ratio recombination recombination events sample score sequence alignment sequence data significant significantly similar species specific split network statistical substitution model substitution rates taxa taxon tree topology values window