Phylogenetic Trees Made Easy: A How-To Manual

INTRODUCTION: READ ME FIRST A Brief Overview of the Second Edition Learn More about the Principles Computer Programs Discussed and Where to Obtain Them Download Files and Utilities from the Website Some Conventions Used in This Book PART 1: TUTORIAL: CREATE A TREE! Why Create Phylogenetic Trees? Obtaining Related Sequences by a BLAST Search Creating the Multiple Alignment Phylogenetic Analysis Drawing the Tree Using TreeView Summary PART 2: BASIC ELEMENTS IN CREATING AND PRESENTING TREES Selecting Homologs: What Sequences Can Be Put onto a Single Tree? Fine Tuning Alignments Major Methods for Creating Trees Data Files Used to Illustrate Methods Using PAUP to Create Trees Creating Maximum Likelihood Protein Trees Using Puzzle Creating Bayesian Trees Using MrBayes Presenting and Printing Your Trees Choosing What Form of a Tree to Publish Making a Tree Pretty: Not Just a Cosmetic Matter DNA or Protein Phylogenies: Which Is Better? PART 3: ADVANCED ELEMENTS IN CONSTRUCTING TREES Reconstructing Ancestral DNA Sequences Using Protein Structure Information to Construct Very Deep Phylogenies Analyzing Trees for Evidence of Adaptive Evolution by Detecting Positive Selection in a Phylogeny PART 4: USING ALTERNATIVE SOFTWARE TO CONSTRUCT AND PRESENT TREES Using PAUP on a Windows or UNIX computer Using PHYLIP Appendix I: File Formats and Their Interconversion Appendix II: Printing Alignments Literature Cited Index to Major Programs Discussed Subject Index