Barry K. Hall
（2007年6月刊行， Sinauer Associates， ISBN:9780878933105 [pbk]）
MEGA / PHYML / MrBayes の教科書として．最尤法とベイズ法はまあいいとしても，最節約法を MEGA ですませるというのはどう考えてもありえないな（それも PAUP* をひっこめてまで）．本書は数年おきに改訂されているが，旧版もお蔵入りさせずに，ちゃんと手元においておく方がきっといいだろう．
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【目次】
Acknowledgments VIIChapter 1. Read Me First! 1
A Brief Overview 1
New and Improved Software 2
The Easy Steps to Making a Tree 2
Learn More about the Principles 4
Computer Programs Discussed and Where to Obtain Them 4
MEGA 5
PHYML 5
MrBayes 5
Codeml 5
Utility Programs 6
Macintosh Only! 6
The Phylogenetic Trees Made Easy Website 6
Register for Updated Information 7
Some Conventions Used in This Book 7Chapter 2. Tutorial: Create a Tree! 9
Why Create Phylogenetic Trees? 9
About this Tutorial 10
MEGA 10
Obtaining Related Sequences by a BLAST Search 11
Aligning the Sequences 22
Making a Neighbor Joining Tree 25
Summary 29Chapter 3. Acquiring and Aligning the Sequences 31
Selecting Homologs: What Sequences Can Be Put onto a Single Tree? 31
Aligning the Sequences 45Interlude I. The Major Methods for Estimating Phylogenetic Trees 57
Distance versus Character-Based Methods 60
Data Files Used to Illustrate Methods 61Chapter 4. Estimating Neighbor Joining Trees 63
Determining the Suitability of the Data for a Neighbor-Joining Tree 63
Estimating the Neighbor-Joining Tree 70
Estimating the Reliability of a Tree 80
What about Protein Sequences? 88Chapter 5. Drawing Phylogenetic Trees 89
Changing the Appearance of a Tree 89
Rooting a Tree 99
Subtrees 103
Saving Trees 105
Captions 105Chapter 6. Parsimony 109
Search Methods 110
Multiple Equally Parsimonious Trees 115
Branch Lengths 117
Level of CNI Search 118
Consensus and Bootstrap Trees 118
What about Protein Sequences? 123Chapter 7. Maximum Likelihood 125
Saving the Data in the PHYLIP Format 125
Installing and Starting PHYML 129
Running PHYML 130
Importing the ML Tree Description into MEGA and Drawing the Tree 132
Tree Reliability Estimated by the Approximate Likelihood Ratio Test Method (aLRT) 136
The Special Case of Zero Length Branches 139
Test Alternative Models 140
What about Protein Sequences? 141Chapter 8. Bayesian Inference of Trees with MrBayes 143
Creating the Execution File 146
What the Statements in the Example MrBayes Block Do 148
What Happens during MrBayes Analysis? 149
The sumt Command 152
What if You Don't Get Convergence? 152
Visualizing the MrBayes Tree 154
What about Protein Sequences? 157
Forthcoming Version of MrBayes 157Interlude II. Which Method Should You Use? 159
Accuracy 160
Ease of Interpretation 160
Time and Convenience 161
Different Estimates of Tree Reliability 162Chapter 9. Reconstructing Ancestral Sequences 165
Using MrBayes to Estimate Ancestral Sequences 166
Correcting Ancestral Sequences for Ancestral Gaps 173Chapter 10. Detecting Adaptive Evolution 177
Using MEGA to Detect Adaptive Evolution 178
Using Codeml to Detect Adaptive Evolution 183Chapter 11. Working with Various Computer Platforms 189
The Line Endings Issue 189
MEGA for Macintosh Users 190
MEGA for Unix/Linux Users 191
MEGA for Windows Users 191
Windows Users: Create a bin Folder and a Path To It 192
A Brief Visit to the Command Prompt Program for Windows Users 194
A Brief Visit to Unix for Macintosh Users 196
PHYML for Windows Users 197
PHYML for Macintosh Users 198
PHYML for Unix/Linux Users 198
MrBayes for Windows Users 198
MrBayes for Macintosh Users 199
MrBayes for Unix/Linux Users 200
Utility Programs for Windows Users 200
Utility Programs for Macintosh Users 200
Utility Programs for Unix and Linux Users 201
Specific Instructions for the Utility Programs in the Download Packages 202
in the Download PackagesAppendix I. File Formats 205
Formats Used by Programs Discussed in this Book 205
Appendix II. Additional Programs 215Literature Cited 221
Index to Major Programs Discussed 223
Subject Index 229
