The Phylogenetic Handbook is a broad introduction to the theory and practice of nucleotide and amino acid phylogenetic analysis. As an unique feature of this book, each chapter contains an extensive practical section, in which step-by-step exercises on real data sets introduce the most widely used phylogeny software including CLUSTAL, PHYLIP, PAUP*, DAMBE, TREE-PUZZLE, TREECON, SplitsTree, TreeView, SimPlot, MEGA2, PAML and BOOTSCANNING. The book provides a strong background in basic topics: the use of sequence databases, alignment algorithms, tree-building methods, estimation of genetic distances, and testing models of evolution.
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Book Description
Editorial Reviews
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"This is a splendid book that does what it says on the cover and presents a practical approach to phylogeny with molecules. ...an excellent tutor for undergraduate or postgraduate study, or for anyone seeking to enter the field." Microbiology Today
"The practice sections throughout the book are exceptionally well-done, making this an extremely valuable feature of this book and one that distinguishes it from the few other phylogenetic texts available...this volume is an excellent resource for phylogenetic analysis for those who are both new and experienced in molecular evolutionary techniques." American Journal of Human Biology
"The practice sections throughout the book are exceptionally well-done, making this an extremely valuable feature of this book and one that distinguishes it from the few other phylogenetic texts available...this volume is an excellent resource for phylogenetic analysis for those who are both new and experienced in molecular evolutionary techniques." American Journal of Human Biology
Book Description
The Phylogenetic Handbook provides a broad introduction to the theory and practice of phylogenetic analysis. It provides a strong grounding in basic topics including the use of sequence databases, alignment algorithms, tree-building methods, estimation of genetic distances, and testing evolutionary models. Each chapter begins with the theory, followed by a practical section, explaining the application of some of the most widely-used phylogeny software including CLUSTAL, PHYLIP, PAUP*, DAMBE, TREE-PUZZLE, TREECON, SplitsTree, TreeView, SimPlot, MEGA2, PAML, and BOOTSCANNING. An invaluable resource for graduate students and professionals in the field of molecular evolution.
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Most Helpful Customer Reviews
14 of 14 people found the following review helpful:
5.0 out of 5 stars
Nicely combine theory and practice,
This review is from: The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny (Hardcover)
I came across this book while doing some phylogenetic analysis and found it very useful.
The first two chapters give some background information on molecular evolution and sequence databases, as well as a downloadable dataset used throughout the book. The real business starts from chapter 3--multiple sequence alignment (MSA). Problems and algorithms of MSA are briefly reviewed. Here you know how CLUSTALW and T-Coffee work. The presentation of the progressive alignment used in CLUSTALW is especially clear. However, other popular programs are not metioned, probably they are not available or not widely used at the time when the book was written. I recommend PROCONS and MUSCLE for protein alignment and DIALIGN-T for both dna and protein alignment. Check them out. Chapter 4 reviews nucleotide substitution model, concise and not much math on continuous-time Markov chain(CTMC). A chart shows the relationship between popular models including GTR, TN93, HKY85, F84, F81, K80 and JC. I like it. To know more details of CTMC of these models, however, you need to consult other books. Exercises using PHYLIP and DAMBE can be found. One someone have the sequence aligned, and genetic/evolutionary distance between them adjusted using say JC, she/he is ready to jump to the next chapter 5 -- Phylogeny Inferrence based on distance methods. Here the outdated UPGMA, mainstream NJ and Fitch-Morgoliash methods are presented by examples, effectively cleaning the fog before these ACRONYM. Bootstrapping and Jacknifing, the two methods for assessing quality of phylogeny, are briefly explained, then progress to exercise using PHYLIP. The next two chapters are maximum-likelihood with TREE-PUZZLE, and Parimony* (* means MP+ML+Distance) in PAUP*. Working on dna or protein sequences sometimes can mean a whole lot of difference, these topics are dealt in chapter 8--Phylogenetic analysis using protein sequences and chapter 9--analysis of nucleotide sequences using TREECON. If you only need to get the tree, you can stop here. The remainign chapters either deal with dN/dS, detecting recomination, or centered on particular software packages including SplitsTree,LAMARC and DAMBE(A heavily used package in this book another is PHYLIP). Overall, the book is comprehensive, well balanced between practice and theory. Though contributed by different authors, the two editors seamlessly wave these chapters into a nice book. Bravo to them! My only concern is book does not cover many widely-used programs, but we, the arduous tree constructors, can find them out by ourselves, do we?
0 of 9 people found the following review helpful:
4.0 out of 5 stars
very good and very practical,
This review is from: The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny (Hardcover)
it is very convenient and handy for a junior student.
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Inside This Book
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First Sentence:
The phenotype of living organisms is always a result of the genetic information that they carry and pass on to the next generation and of the interaction with the environment. Read the first page Key Phrases - Statistically Improbable Phrases (SIPs): (learn more)
intersubtype variation, bootscanning method, mega format, tetrapod data, substitution saturation, nondegenerate site, invariable sites, alternative phylogenetic hypotheses, sequence input file, single codon sites, substitution rate calibration, nucleotide substitution models, transversional substitutions, compatible splits, negative branch lengths, nonsynonymous differences, different tree topologies, nucleotide frequencies, nonsynonymous sites, degenerate sites, unaligned sequences, rate heterogeneity, possible quartets, different evolutionary models, specific tree topology Key Phrases - Capitalized Phrases (CAPs): (learn more)
Journal of Molecular Evolution, Van de Peer, Sinauer Associates, New York, Los Alamos, Journal of Molecular Biology, Journal of Virology, Systematic Zoology, Academic Press, Computer Applications, Systematic Biology, Codon Amino, Monte Carlo, Nucleic Acids Research, Department of Genetics, Marco Salemi, University of Washington, Kluwer Academic Publishers, Molecular Systematics, Phylogeny Inference Package, Blackwell Science, Cambridge University Press, Joe Felsenstein, Mammalian Protein Metabolism, Phylogenetic Approach New!
Books on Related Topics | Concordance | Text Stats Browse Sample Pages:
Front Cover | Table of Contents | First Pages | Index | Back Cover | Surprise Me!
The phenotype of living organisms is always a result of the genetic information that they carry and pass on to the next generation and of the interaction with the environment. Read the first page Key Phrases - Statistically Improbable Phrases (SIPs): (learn more)
intersubtype variation, bootscanning method, mega format, tetrapod data, substitution saturation, nondegenerate site, invariable sites, alternative phylogenetic hypotheses, sequence input file, single codon sites, substitution rate calibration, nucleotide substitution models, transversional substitutions, compatible splits, negative branch lengths, nonsynonymous differences, different tree topologies, nucleotide frequencies, nonsynonymous sites, degenerate sites, unaligned sequences, rate heterogeneity, possible quartets, different evolutionary models, specific tree topology Key Phrases - Capitalized Phrases (CAPs): (learn more)
Journal of Molecular Evolution, Van de Peer, Sinauer Associates, New York, Los Alamos, Journal of Molecular Biology, Journal of Virology, Systematic Zoology, Academic Press, Computer Applications, Systematic Biology, Codon Amino, Monte Carlo, Nucleic Acids Research, Department of Genetics, Marco Salemi, University of Washington, Kluwer Academic Publishers, Molecular Systematics, Phylogeny Inference Package, Blackwell Science, Cambridge University Press, Joe Felsenstein, Mammalian Protein Metabolism, Phylogenetic Approach New!
Books on Related Topics | Concordance | Text Stats Browse Sample Pages:
Front Cover | Table of Contents | First Pages | Index | Back Cover | Surprise Me!
Citations (learn more)
This book cites 25
books:
See all 25 books this book cites
- Molecular Systematics, Second Edition by David M. Hillis on 6 pages
- Mammalian Protein Metabolism: v. 1 by H.N. Munro on 5 pages
- Data Analysis in Molecular Biology and Evolution by Xuhua Xia on 5 pages
- Molecular Biology by Hd Kumar on 4 pages
- Atlas of Protein Sequence and Structure (Vol 5, Supplement 3) by Margaret O. Dayhoff on page 69, page 233, and page 280
See all 25 books this book cites
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