Phylogenetic Trees Made Easy: A How-To Manual for Molecular Biologists [Illustrated] [Paperback]

Barry G. Hall (Author)

Book Description

ISBN-10: 0878933115 | ISBN-13: 978-0878933112 | Publication Date: March 2001 | Edition: illustrated edition

This text is intended to aid beginners in getting started creating phylogenetic trees from protein or nucleic acid sequence data. Although aimed at molecular and cell biologists who may not be familiar with phylogenetic or evolutionary theory, it also serves students who may be familiar with phylogenetic theory but unfamiliar with the tools used to apply that theory. The reader is led, step-by-step, through identifying sequences that are homologous to a sequence of interest, downloading those sequences from databases, creating multiple alignments, and using several different methods to construct trees.

Editorial Reviews

About the Author

BARRY G. HALL is Professor of Biology at the University of Rochester.

Product Details

• Paperback: 208 pages
• Publisher: Sinauer Associates Inc; illustrated edition edition (March 2001)
• Language: English
• ISBN-10: 0878933115
• ISBN-13: 978-0878933112
• Product Dimensions: 9.6 x 6.9 x 0.5 inches
• Shipping Weight: 1.4 pounds
• Average Customer Review: 4.3 out of 5 stars  See all reviews (3 customer reviews)
• Amazon Best Sellers Rank: #1,072,495 in Books (See Top 100 in Books)

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Customer Reviews

Most Helpful Customer Reviews

2 of 2 people found the following review helpful:

4.0 out of 5 stars Step-by-step instruction with downloadable input data files, January 20, 2004

By 

Seungwoo Hwang (Albany, NY USA) - See all my reviews
(REAL NAME)   

This review is from: Phylogenetic Trees Made Easy: A How-To Manual for Molecular Biologists (Paperback)

What I liked about this slim book is that, as in Chapter 1, it first provides you with data files with which you can build phylogenetic trees, then guides you through step by step. Also, I liked its concise overview about phylogenetics.

However, Chapter 2 does not come with such data files. It only provides you with templates. Why?

Also what you should be aware before ordering this book is that the explanations on this book assume that you;
(1) have a copy of PAUP (which is not a free software), and;
(2) are running PAUP on Mac OS.

So, if you are running PAUP on Windows/UNIX and do not have any access to Mac, you probably don't want to buy this book. PAUP manual should better serve you.

2 of 2 people found the following review helpful:

4.0 out of 5 stars MrBayes and Paup* manual, September 27, 2003

By A Customer

This review is from: Phylogenetic Trees Made Easy: A How-To Manual for Molecular Biologists (Paperback)

I picked up this book because I was trying to learn MrBayes on my own with little success. With new versions of MrBayes, this book is already out of date and I encountered some frustration with my Nexus code being wrong, but between the help function, a lot of trial and error, and Hall's book I managed to successfully analyze my data using Bayesian analysis! I highly recommend it for the "cookbook" appeal-- software like PAUP and MrBayes can be difficult to learn on your own, and it's nice to have someone explain it step by step. I would have liked some instruction on saturation curves, but the book is fairly complete otherwise. MacClade is not mentioned, probably because it is more user-friendly than the programs included. PTME has been criticized for some incorrect statements in the book regarding theory, but I would expect students to use this book for practice more than theory. Overall, a great little manual to have on the shelf.

5.0 out of 5 stars good orientation, July 25, 2004

By 

Parby Grylam "Grylam" (Las Vegas, NV USA) - See all my reviews

Amazon Verified Purchase

This review is from: Phylogenetic Trees Made Easy: A How-To Manual for Molecular Biologists (Paperback)

I've been looking around for a good introduction to bioinformatics software for some months now. I have only read 37 pages, but that was worth the purchase price and I am enthusiastic about reading on. Hall does a very nice job of explaining the uses of Blast and ClustalX, differentiating among the various versions and showing how protein analysis differs from DNA analysis. (His focus is proteins.) He takes you step by step through an analysis and explains the information available on the screen at each step. He tells you how to manage the resulting input and results files, and he even explains choices of penalties for gaps. All very clear.