Table of contents for Phylogenetic trees made easy : a how-to manual / Barry G. Hall.

Bibliographic record and links to related information available from the Library of Congress catalog.

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1. Read Me First!
A Brief Overview of the Third Edition
Learn More about the Principles
Computer Programs Discussed and Where to Obtain Them
Files and Utilities on the ?Phylogenetics Made Easy? Website
2. Tutorial: Create a Tree
Why Create Phylogenetic Trees?
About This Tutorial
MEGA
Obtaining Related Sequences by a BLAST Search
Aligning Sequences by ClustalW within MEGA
Creating a Neighbor Joining Tree with MEGA
Drawing and Printing the Tree
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
4. Estimating Neighbor Joining Trees
Determining the Suitability of the Data for a Neighbor Joining Tree
Estimating the Neighbor Joining Tree
Estimating the Reliability of a Tree
What about Protein Sequences?
5. Drawing Phylogenetic Trees
Changing the Appearance of a Tree
Different Formats
Labeling Branches
Adjusting the Size of the Tree
Changing Label Fonts, etc.
Rooting a Tree
Subtrees
Saving Trees
Exporting Tree Descriptions
Importing Tree Descriptions
Captions
6. Estimating Parsimony Trees with MEGA
Search Methods
Multiple Equally Parsimonious Trees
Branch Lengths
Level of CNI Search
Consensus and Bootstrap Trees
What about Protein Sequences?
7. Estimating Maximum Likelihood Trees with PHYML
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 Don?t Get Convergence?
Visualizing the MrBayes Tree
What about Protein Sequences?
Interlude II. Which Method Should You Use?
9. Reconstructing Ancestral Sequences
Using MrBayes to Estimate Ancestral Sequences
Correcting Ancestral Sequences for Ancestral Gaps
10. Detecting Adaptive Evolution
Using MEGA
Using Codeml from the PAML Package
11. Working with Various Computer Platforms
The Line Endings Issue
Using MEGA for Macintosh Users
Using 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
Perl Scripts for Windows Users
Perl Scripts for Macintosh, Unix, and Linux Users
Specific Instructions for the Perl Scripts in the Download Packages
Appendix I. File Formats
Appendix II. Useful Websites
Literature Cited

Library of Congress Subject Headings for this publication:

Phylogeny -- Data processing.