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

Philippe Lemey , Marco Salemi , Anne-Mieke Vandamme
4.8 out of 5 stars  See all reviews (12 customer reviews)

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Book Description

April 20, 2009 0521730716 978-0521730716 2nd
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.

Frequently Bought Together

The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing + Phylogenetic Trees Made Easy: A How To Manual, Fourth Edition + Phylogenetics: Theory and Practice of Phylogenetic Systematics
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Editorial Reviews

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

Book Description

With a stronger focus on hypothesis testing, elaborate practical sections and recent versions of sequence analysis and software, this edition includes six new chapters. Topics on Bayesian inference, tree topology testing and the impact of recombination on phylogenies have been added as well as a detailed section on molecular adaptation.

Product Details

  • Paperback: 750 pages
  • Publisher: Cambridge University Press; 2nd edition (April 20, 2009)
  • Language: English
  • ISBN-10: 0521730716
  • ISBN-13: 978-0521730716
  • Product Dimensions: 6.3 x 8.3 x 1.5 inches
  • Shipping Weight: 3.1 pounds (View shipping rates and policies)
  • Average Customer Review: 4.8 out of 5 stars  See all reviews (12 customer reviews)
  • Amazon Best Sellers Rank: #474,998 in Books (See Top 100 in Books)

Customer Reviews

4.8 out of 5 stars
(12)
4.8 out of 5 stars
Most Helpful Customer Reviews
13 of 13 people found the following review helpful
5.0 out of 5 stars Both theory and practice October 15, 2009
Format:Paperback|Verified Purchase
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.
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6 of 6 people found the following review helpful
5.0 out of 5 stars Strikes a good balance March 26, 2010
Format:Paperback|Verified Purchase
In my opinion, this book strikes a good balance between being a reference book and a text book.
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5 of 5 people found the following review helpful
5.0 out of 5 stars User-friendly and comprehensive February 24, 2011
Format:Paperback|Verified Purchase
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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3 of 3 people found the following review helpful
5.0 out of 5 stars One of the best books on phylogenetics I've seen August 21, 2010
Format:Paperback|Verified Purchase
This is a clearly written well organized book. Great for reference or even a basic book on phylogenetics, a field with few really good overview books good for a student or more experienced researcher (IMHO).
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2 of 2 people found the following review helpful
5.0 out of 5 stars Phylogenetic handbook it is... March 21, 2011
Format:Paperback|Verified Purchase
This is an equally great book for people who are starters as well as people who are working in the field of phylogenetics. Starts with a nice intro to the field and gradually builds up to talk about different aspects of molecular phylogenetics including PRACTICE exercises. Definitely recommend people to buy it.
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2 of 2 people found the following review helpful
5.0 out of 5 stars Concise and informative January 29, 2011
Format:Paperback|Verified Purchase
I used this book to complete an independent study in phylogenetic reconstruction, and this book was really quite good. It gives, in some cases, more detail than needed, going into the derivation of all the mathematics behind phylogenetic algorithms. I've found it to be quite readable however, and a very usable text. This will likely sit on my desk as a reference text for many years to come. Overall a good purchase.
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