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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.