Phylogenetic Trees Made Easy: A How-To Manual (5th Edition)

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Cover Front Matter Copyright Page Dedication Acknowledgments Table of Contents Chapter 1 Read Me First! New and Improved Software Just What Is a Phylogenetic Tree? Estimating Phylogenetic Trees: The Basics Beyond the Basics Learn More about the Principles About Appendix VI: F.A.Q. Computer Programs and Where to Obtain Them MEGA7 BEAST FigTree codeml SplitsTree and Dendroscope Graphviz Utility Programs Text Editors Acknowledging Computer Programs Website The Chapter 2 Tutorial: Estimate a Tree Why Create Phylogenetic Trees? About this Tutorial Macintosh and Linux users A word about screen shots Search for Sequences Related to Your Sequence Decide Which Related Sequences to Include on Your Tree Establishing homology To include or not to include, that is the question Download the Sequences Align the Sequences Make a Neighbor Joining Tree Summary Chapter 3 Acquiring the Sequences Background Problems arising from the vast size of the sequence databases The query sequences Hunting Homologs: What Sequences Can Be Included on a Single Tree? Becoming More Familiar with BLAST BLAST help Using the Nucleotide BLAST Page Using BLAST to Search for Related Protein Sequences Finalizing Selected Sequences for a Tree Problems adding coding sequences of protein homologs to the Alignment Explorer Adding Sequences to and Removing Sequences from the Alignment Explorer Add a sequence Import a file of sequences Delete a sequence Other Ways to Find Sequences of Interest (Beware! The Risks Are High) Chapter 4 Aligning the Sequences Aligning Sequences with MUSCLE Examine and Possibly Manually Adjust the Alignment Trim excess sequence Eliminate duplicate sequences Check Average Identity to Estimate Reliability of the Alignment Codons: Pairwise amino acid identity Non-coding DNA sequences Increasing Alignment Speed by Adjusting MUSCLE’s Parameter Settings How MUSCLE works Adjusting parameters to increase alignment speed Aligning Sequences with ClustalW Aligning Sequences with GUIDANCE2 Viewing the results Eliminate unreliable parts of the alignment Saving the GUIDANCE2 alignment Chapter 5 Major Methods for Estimating Phylogenetic Trees Distance versus Character-Based Methods Chapter 6 Neighbor Joining Trees Using MEGA7 to Estimate a Neighbor Joining Tree Determine the suitability of the data for a Neighbor Joining tree Estimate the tree Unrooted and Rooted Trees Estimating the Reliability of a Tree What about Protein Sequences? Chapter 7 Drawing Phylogenetic Trees Changing the Appearance of a Tree The Options dialog Branch styles Fine-tuning the appearance of a tree Rooting a Tree Finding an outgroup Subtrees Saving Trees Saving a tree description Saving a tree image Captions Chapter 8 Parsimony MP Search Methods Using SeaView for Parsimony Estimating a bootstrap tree in SeaView Using MEGA to draw the tree estimated by SeaView Chapter 9 Maximum Likelihood ML Analysis Using MEGA Test alternative models Estimating the Reliability of an ML Tree by Bootstrapping What about Protein Sequences? Chapter 10 Bayesian Inference of Trees Using BEAST BEAST: An Overview Installing BEAST Prepare the Input Alignment File Run BEAUti Running BEAST Run Tracer Burnin Run TreeAnnotator What about Protein Sequences? Visualizing the BEAST Tree The icons above the tree Chapter 11 Which Method Should You Use? Criteria to Consider Accuracy Ease of interpretation Time and convenience Results of the Major Methods Chapter 12 Working with Various Computer Platforms Command-line Programs MEGA on the Macintosh Platform Navigating among folders on the Mac Printing trees and text from MEGA The Line Endings Issue Running the Utility Programs Chapter 13 Phylogenetic Networks Why Trees Are Not Always Sufficient Unrooted and Rooted Phylogenetic Networks Using SplitsTree to Estimate Unrooted Phylogenetic Networks Estimating networks from alignments Rooting an unrooted network Estimating networks from trees Consensus networks Supernetworks Using Dendroscope to Estimate Rooted Networks from Rooted Trees Chapter 14 Minimum Spanning Trees Phylogenetic Trees! Minimum Spanning Trees Are Why Use Minimum Spanning Trees? Origin of MSTs and the Issue of Reliability What is a minimum spanning tree? Using MSTgold to Estimate MSTs The MSTgold input files Two ways for MSTgold to calculate the initial distance matrix Running MSTgold with the ebgC data The MSTgold output Bootstrapping MSTgold Exporting MSTs from Graphviz An Alternative Data Set to Illustrate Some Additional Features of MSTgold An Alternative to Graphviz: Hypercube Chapter 15 Time Trees Preparations to Estimate a Time Tree Estimating a Time Tree Viewing the Relative Time Tree An Absolute Time Tree Effect of more calibration points on absolute time trees Postscript Chapter 16 Reconstructing Ancestral Sequences Using MEGA to Estimate Ancestral Sequences by Maximum Likelihood Create the alignment Construct the phylogeny Examine the ancestral states at each site in the alignment Estimate the ancestral sequence Calculating the ancestral protein sequence and amino acid probabilities How Accurate Are the Estimated Ancestral Sequences? Chapter 17 Detecting Adaptive Evolution Effect of Alignment Accuracy on Detecting Adaptive Evolution Using MEGA to Detect Adaptive Evolution is an interesting example for considering adaptive evolution Why Detecting overall selection Detecting selection between pairs Finding the region of the gene that has been subject to positive selection Using codeml to Detect Adaptive Evolution Installation Run codeml Questions that underlie the models A closer look at ebgC_1.out Summary Postscript Compiling PAML yourself and running codeml without Chapter 18 Estimating Phylogenetic Trees from Whole Genome Sequences The Pan-Genome Problem kSNP: An Alternative to Genome Alignment kSNP 2.0 kChooser FCK Tree accuracy Always run kChooser before running kSNP Using kSNP3 The steps in estimating phylogenetic trees from WGS using kSNP3 Chapter 19 Some Final Advice: Learn to Program Appendix I File Formats and Their Interconversion Format Descriptions The MEGA format The FASTA format The Nexus format The PHYLIP format Interconverting Formats FastaConvert, MEGA, and SeaView Appendix II Text Editors Mac OS X: TextWrangler Windows: Notepad++ Linux: Gedit Appendix III The Command-line Environment Introduction and History Terminal and Command Prompt: The Apps for Accessing the Command-line Environment The current directory Entering Commands Navigating in Terminal The Magic Trick Command ( What Is in the CWD? The The -l option The -a option The permissions column The Command in Command Prompt Some Other Important Commands Copy a file Move a file Rename a file Make a directory Remove a directory Remove a file Print the contents of a file to the screen Clear the screen Appendix IV Installing and Running Command-line Programs Installing Command-line Programs Mac OS X / Linux Windows Running Command-line Programs An example The line endings issue The example command line Error checking Appendix V Additional Programs Appendix VI Frequently Asked Questions Literature Cited Index to Major Program Discussions Subject Index