The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing

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Philippe Lemey, Marco Salemi, Anne-Mieke Vandamme
Cambridge University Press, Mar 26, 2009 - Science
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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.
 

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This textbook comes with online data sets to be used with the tutorials in each chapter. The data sets can be extremely helpful because different programs take different input formats (FASTA, NEXUS, extended-NEXUS, etc) and it can be frustrating for new users to figure out the format(s) that each program will accept. The authors of each chapter were carefully chosen for their expertise in the subject area and many of the chapters were written by the actual authors of the software packages being described. Many of the chapters cover very sophisticated analyses that are beyond the needs of most evolutionary biologists, but there are also chapters covering the more simple and straightforward methods that EVERY biology student and researcher should become familiar with. 

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
Practice
576
Estimating population genetic parameters
592
Practice
598
Assessing substitution saturation with DAMBE
615
Practice
624
2 Split networks A tool for exploring complex evolutionary
631
Practice
642
Glossary
654
References
672
Index
709
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About the author (2009)

Philippe Lemey is a FWO postdoctoral researcher at the Rega Institute, Katholieke Universiteit Leuven, Belgium, where he completed his PhD in Medical Sciences. He has been an EMBO fellow and a Marie-Curie fellow in the Evolutionary Biology Group at the Department of Zoology, University of Oxford. His research focuses on molecular evolution of viruses by integrating molecular biology and computational approaches.

Marco Salemi is a postdoctoral scientist in the Medical Faculty at the Katholieke Universiteit, Belgium. He currently holds a research position at the University of California, Irvine, where he works on epidemiological virology and phylogenetic analysis, focusing on the molecular epidemiology of human pathogenic viruses, such as HIV and HCV. He is supported by the Fund for Scientific Research - Flanders, Belgium.

Anne-Mieke Vandamme is a Full Professor in the Medical Faculty at the Katholieke Universiteit, Belgium, working in the field of clinical and epidemiological virology. Her laboratory investigates treatment responses in HIV-infected patients and is respected for its scientific and clinical contributions on virus-drug resistance. Her laboratory also studies the evolution and molecular epidemiology of human viruses such as HIV and HTLV.

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