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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.
- Sales Rank: #791407 in Books
- Brand: Brand: Cambridge University Press
- Published on: 2009-04-20
- Original language: English
- Number of items: 1
- Dimensions: 9.72" h x 1.34" w x 6.85" l, 3.20 pounds
- Binding: Paperback
- 750 pages
- Used Book in Good Condition
Review
"This impressive handbook provides unparalleled coverage of the practice of turning genetic data into sensible statements about evolutionary history and processes. Intended as a hands-on resource for the student or professional scientists who wishes to master basic phylogenetic concepts and get to grips with the software - in this regard it succeeds admirably."
- Mike Steel, Biometrics
About the Author
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.
Most helpful customer reviews
13 of 13 people found the following review helpful.
Both theory and practice
By A. Saunders
This book is an excellent introduction to the basis principles of phylogenetics. The text is especially good for the practicing biologist as it also has a practical component that applies these theoretical concepts. There are downloadable exercises and walk through examples using many of the commonly used phylogentic software. A solid book for the beginner to intermediate practitioner.
7 of 7 people found the following review helpful.
Strikes a good balance
By Edward A. Salinas
In my opinion, this book strikes a good balance between being a reference book and a text book.
5 of 5 people found the following review helpful.
User-friendly and comprehensive
By Guinevere Lee
This textbook introduces concepts that cover from a basic/beginner level to a very advance level, making it a very handy reference. I am not familiar with phylogenetic analysis nor can I do computer programming, and so phylogenetic analysis has always been a mystery to me even though I have always been curious about how exactly Blast and ClustalW work. This handbook has demystified much of them for me. I think the best part about this handbook is that it explains concepts using a friendly tone and goes step-by-step from simple overview to difficult concepts. And therefore I always feel the liberty to jump sections and read what I need/want to know. I particularly love the hands-on practice guides!
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