Phylogenetic Trees Made Easy helps the reader get started in 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 are 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 these sequences from databases, creating multiple alignments, and using several different methods to construct trees.
Learn More boxes present background on the various concepts and methods, and a website provides files needed for working through the tutorials in the text as well as additional software that facilitates some of the methods discussed.
Key Changes to the Third Edition
* Over 90% of the text and screenshots are new.
* A new program, MEGA, that has dramatically simplified and sped up the most tedious parts of making treessearching for and downloading sequences, aligning those sequences, and getting them into suitable formatsis introduced as the primary tool for constructing trees.
* PHYML, another new program that has sped up the Maximum Likelihood method by more than 100-fold, making it a practical alternative to other methods, is introduced.
* Chapter 9 is devoted to a detailed method for reconstructing very ancient ancestral sequences, and software to facilitate that method is made available on the website.
* Chapter 10 speaks to detecting adaptive evolution.
* The final chapter comprises detailed instructions for working with programs on Macintosh, Windows, and Unix platforms.
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Table of Contents
1. Read Me First!
* A Brief Overview
* New and Improved Software
* The Easy Steps to Making a Tree
* Learn More about the Principles
* Computer Programs Discussed and Where to Obtain Them
* The Phylogenetic Trees Made Easy Website
* Register for Updated Information
* Some Conventions Used in This Book
2. Tutorial: Create a Tree!
* Why Create Phylogenetic Trees?
* About This Tutorial
* MEGA
* Obtaining Related Sequences by a BLAST Search
* Aligning the Sequences
* Making a Neighbor-Joining Tree
* Summary
3. Acquiring and Aligning the Sequences
* Selecting Homologs: What Sequences Can Be Put on a Single Tree?
* Aligning the Sequences
INTERLUDE I. THE MAJOR METHODS FOR ESTIMATING PHYLOGENETIC TREES
* Distance versus Character-Based Methods
* Data Files Used to Illustrate Methods
4. Neighbor-Joining Trees
* Determine the Suitability of the Data for a Neighbor-Joining Tree
* Estimate the Neighbor-Joining Tree
* Estimating the Reliability of a Tree
* What about Protein Sequences?
5. Drawing Phylogenetic Trees
* Changing the Appearance of a Tree
* Rooting a Tree
* Subtrees
* Saving Trees
* Captions
6. Parsimony
* Search Methods
* Multiple Equally Parsimonious Trees
* Branch Lengths
* Level of CNI Search
* Consensus and Bootstrap Trees
* What about Protein Sequences?
7. Maximum Likelihood
* Saving the Data in PHYLIP Format
* Installing and Starting PHYML
* Running PHYML
* Importing the ML Tree Description into MEGA and Drawing the Tree
* Tree Reliability Estimated by the approximate Likelihood Ratio Test Method (aLRT)
* The Special Case of Zero Length Branches
* Test Alternative Models
* What about Protein Sequences?
8. Bayesian Inference of Trees with MrBayes
* Creating the Execution File
* What the Statements in the Example MrBayes Block Do
* What Happens during MrBayes Analysis?
* The sumt Command
* What if You Dont Get Convergence?
* Visualizing the MrBayes Tree
* What about Protein Sequences?
* Forthcoming Version of MrBayes
INTERLUDE II. WHICH METHOD SHOULD YOU USE?
* Accuracy
* Ease of Interpretation
* Time and Convenience
* Different Estimates of Tree Reliability
9. Reconstructing Ancestral Sequences
* Using MrBayes to Estimate Ancestral Sequences
* Correcting Ancestral Sequences for Ancestral Gaps
10. Detecting Adaptive Evolution
* Using MEGA to Detect Adaptive Evolution
* Using Codeml to Detect Adaptive Evolution
11. Working with Various Computer Platforms
* The Line Endings Issue
* MEGA for Macintosh Users
* MEGA for Unix/Linux Users
* Windows Users: Create a bin Folder and a Path to It
* A Brief Visit to the Command Prompt Program for Windows Users
* A Brief Visit to Unix for Macintosh Users
* PHYML for Windows Users
* PHYML for Macintosh Users
* PHYML for Unix/Linux Users
* MrBayes for Windows Users
* MrBayes for Macintosh Users
* MrBayes for Unix/Linux Users
* Utility Programs for Windows Users
* Utility Programs for Macintosh Users
* Utility Programs for Linux and Unix Users
* Specific Instructions for the Utility Programs in the Download Packages
Appendix I. File Formats and Their Interconversion
Appendix II. Additional Programs
Literature Cited
Index to Major Programs Discussed
Subject Index