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Rating: 
Summary: MrBayes and Paup* manual
Review: 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 With new versions of MrBayes, this book is already out of date and I encountered some frustration with my Nexus code being wrong, but between the help function, a lot of trial and error, and Hall's book I managed to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.
Rating: 
Summary: good orientation
Review: 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.
Rating:
Summary: Delivers
Review: This book delivers what it promises. It says right on its first page that it is not a textbook on phylogetic tree building, but a "cookbook" that teaches you step by step how to build the trees with the current tools available. What I liked the most was the available downloads from the publisher's web page. You can check your results against the author's, skip a section but still get the data you would get from it so you can do the next section and get program lines for you to customize. A simple, well written, hands-on book for us starting Evolutionary Biology types.
Rating:
Summary: Step-by-step instruction with downloadable input data files
Review: 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? And just in case you are not aware, you need to have PAUP installed on your computer to go through this book, and PAUP is not a free software.
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