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Phylogenetic Trees Made Easy

A How-To Manual

Fifth Edition

Barry G. Hall

Publication Date - October 2017

ISBN: 9781605357102

368 pages
Paperback

In Stock

Retail Price to Students: $67.95

Helps the reader get started in creating phylogenetic trees from protein or nucleic acid sequence data.

Description

Phylogenetic Trees Made Easy, Fifth Edition 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 have a theoretical understanding of phylogenetics but need guidance in transitioning to a practical application of the methodology. The reader is led, step by step, through identifying and acquiring the sequences to be included in a tree, aligning the sequences, estimating the tree by one of several methods, and drawing the tree for presentation to an intended audience. "Learn More" boxes present background on the various concepts and methods.

Note: Files needed for working through the tutorials in the text, as well as additional software that facilitates some of the methods discussed, can be accessed via the Ancillary Resource Center link on this page.

New to this Edition

  • The release of this edition was prompted by the development of a new version of the phylogenetic software MEGA. MEGA7 has several capabilities that were not present in MEGA5.
  • Three new chapters (Minimum Spanning Trees; Time Trees; and Estimating Phylogenetic Trees from Whole Genome Sequences) address important advanced topics.
  • The chapter on Bayesian Inference is now illustrated using the program BEAST, a WYSIWYG program with a familiar application environment.
  • Three new Appendices discuss text editors, the many command-line programs that are available, and facilitating the installation of those programs in the Windows, Mac, and Linux environments.
  • New screen shots throughout show the current versions of all software. These illustrations are in full color, enabling readers to more easily identify elements in which color plays an important informational role.
  • This edition is organized into 19 (versus 16) chapters, to better isolate important topics.

Features

  • "Learn More" boxes present background on the various concepts and methods.
  • Files needed for working through the tutorials in the text, as well as additional software that facilitates some of the methods discussed, can be accessed via the Ancillary Resource Center link on this page.

About the Author(s)

Barry G. Hall is Director of the Bellingham Research Institute, Adjunct Professor of Genomics and Bioinformatics at the Allegheny-Singer Research Institute's Center for Genomic Sciences, and Professor Emeritus of Biology, University of Rochester. A founding member of the Society for Molecular Biology and Evolution, he has served as Editor-in-Chief of its journal, Molecular Biology and Evolution, and on the Editorial Boards of Genetics, the Journal of Molecular Evolution, and the Journal of Bacteriology. His current research interests include the molecular epidemiology of bacterial pathogens and application of genomic analysis to rapid prediction of antibiotic sensitivity in clinical applications. He has continued to publish 2-3 papers a year since his retirement in 2003.

Previous Publication Date(s)

April 2011
June 2007

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
    MEGA 7
    BEAST
    FigTree
    codeml
    SplitsTree and Dendroscope
    Graphviz
    Utility Programs
    Text Editors
    Acknowledging Computer Programs
    The
    Phylogenetic Trees Made Easy Website

    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
    Box: Learn More About Tree-Searching Methods
    Distance versus Character-Based Methods
    Box: Learn More About Distance Methods

    CHAPTER 6 NEIGHBOR JOINING TREES
    Using MEGA7 to Estimate a Neighbor Joining Tree
    Box: Learn More About Phylogenetic Trees
    Determine the suitability of the data for a Neighbor Joining tree
    Estimate the tree
    Box: Learn More About Evolutionary Models
    Unrooted and Rooted Trees
    Estimating the Reliability of a Tree
    Box: Learn More About Estimating the Reliability of Phylogenetic Trees
    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
    Box: Learn More About 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
    Box: Learn More About 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
    Box: Learn More About Bayesian Inference
    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
    Box: Learn More About 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

    NEW! CHAPTER 14 MINIMUM SPANNING TREES
    Minimum Spanning Trees Are Not Phylogenetic Trees!
    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

    NEW! 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
    Why ebgC is an interesting example for considering adaptive evolution
    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 pamlX

    NEW! 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

    NEW! APPENDIX II TEXT EDITORS
    Mac OS X: TextWrangler
    Windows: Notepad++
    Linux: Gedit

    NEW! 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
    What Is in the CWD? The ls Command (§ dir)
    The -l option
    The -a option
    The permissions column
    The chmod command
    §The dir 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

    NEW! 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
    The output file(s)
    Error checking

    APPENDIX V ADDITIONAL PROGRAMS

    APPENDIX VI FREQUENTLY ASKED QUESTIONS

    LITERATURE CITED

    INDEX TO MAJOR PROGRAM DISCUSSIONS

    SUBJECT INDEX

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