Phylogenetics Trees Made Easy

by Hall, Barry G.

• ISBN13: 9780878933112
• ISBN10: 0878933115
• Format: Paperback
• Copyright: 2001-03-01
• Publisher: Sinauer Associates Inc

Summary

Phylogenetic Trees Made Easy is a "how-to" book, intended to aid beginners in getting started 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 may be familiar with phylogenetic theory yet unfamiliar with the tools used to apply that theory. The reader is led, step by step, through identifying sequences that are homologous to a sequence of interest, downloading those sequences from databases, creating multiple alignments, and using several different methods to construct trees. "Learn More" boxes present more detailed background on these methods, and an accompanying website provides the various files needed for working through the tutorials in the text.

Table of Contents

Introduction: Read Me First	1	(1)
A Brief Overview	2	(1)
Learn More About the Principles	2	(1)
Computer Programs Discussed and Where to Obtain Them	3	(2)
ClustalX	3	(1)
PAUP*	3	(1)
MrBayes	3	(1)
Puzzle	4	(1)
CodonAlign	4	(1)
Programs That Are Not Discussed but That Might Be Useful	4	(1)
Download Files and Utilities from the Web Site	5	(1)
Some Conventions Used in This Book	6	(1)
Tutorial: Create a Tree!	7	(62)
Why Create Phylogenetic Trees?	7	(1)
Obtaining Related Sequences by a BLAST Search	8	(11)
Step 1	9	(1)
Step 2	10	(1)
Step 3	11	(6)
Downloading the Selected Sequences	17	(2)
Creating the Multiple Alignment	19	(18)
Creating the Input File	20	(2)
Getting the Data into ClustalX	22	(1)
Some General Comments about Creating Alignments	23	(1)
Setting the Alignment Parameters	23	(5)
Creating the Alignment	28	(1)
Refining and Improving the Alignment	29	(5)
Aligning New Sequences to an Existing Alignment or Aligning Two Existing Alignments	34	(3)
Phylogenetic Analysis	37	(1)
Methods for Constructing Phylogenies	27	(10)
Using PAUP* to Create a Tree	37	(11)
Creating the Input File	38	(2)
Creating a Neighbor-Joining Tree with PAUP*	40	(4)
Exactly What Is a Phylogenetic Tree?	44	(4)
Learn More About Phylogenetic Trees	48	(6)
Placing the Root of a Tree	52	(2)
Learn More About Rooting Phylogenetic Trees	54	(6)
Bootstrapping a Tree	58	(2)
Learn More About Estimating the Reliability of Phylogenetic Trees	60	(9)
Saving and Using Tree Files	64	(5)
Additional Methods for Creating Trees	69	(46)
Which Method Should You Use?	69	(1)
Learn More About Tree-Searching Methods	70	(3)
Distance vs. Character-Based Methods	73	(1)
Learn More About Distance Methods	74	(3)
Creating Parsimony Trees Using PAUP*	77	(1)
Learn More About Parsimony	78	(8)
Creating Maximum Likelihood DNA Trees Using PAUP*	86	(1)
Learn More About Maximum Likelihood	87	(4)
Step 1: Set Up the Data File	89	(1)
Step 2: Create and Run an Execution File	90	(1)
Learn More About Evolutionary Models	91	(5)
Creating Maximum Likelihood Protein Trees Using Puzzle	96	(2)
Using MrBayes to Create Bayesian DNA Trees	98	(2)
Creating the Execution File	99	(1)
Learn More About Bayesian Analysis	100	(15)
Getting Help	103	(3)
What the Statements in the Example MrBayes Block Do	106	(2)
The mcmcp Command	108	(1)
What About the Other Parameters Under Iset?	109	(1)
Summarizing MrBayes	109	(1)
Sample Blocks for MrBayes	110	(1)
Reliability of the Consensus Tree	111	(4)
Presenting and Printing Your Trees	115	(18)
To Root or Not to Root?	115	(11)
Midpoint Rooting	118	(2)
Rooting with an Outgroup	120	(6)
Choosing What Form of a Tree to Publish	126	(1)
Making a Tree Pretty: Not Just a Cosmetic Matter	126	(7)
Making an Unruly Phylogram Pretty	128	(2)
Indicating Branch Lengths on Trees	130	(3)
Fine-Tuning Alignments	133	(4)
Using MrBayes to Reconstruct Ancestral DNA Sequences	137	(8)
Dealing with Some Common Problems	145	(8)
DNA or Protein Phylogenies: Which Is Better?	145	(1)
Using CodonAlign for Protein Coding Sequences	146	(3)
Running CodonAlign	147	(1)
The Output File	148	(1)
Error Messages	148	(1)
Use of the Source Code	148	(1)
The Effects of Including Nonhomologous Sequences	149	(4)
Using BLAST to Assess the Homology of Two Sequences	150	(3)
Appendix I File Formats and Their Interconversion Using PAUP*	153	(10)
Formats Used by Programs Discussed in this Book	153	(4)
The FASTA Format	154	(1)
The Clustal Format	154	(1)
The Nexus Format	155	(2)
Other File Formats	157	(4)
Phylip 3.x	157	(2)
The GCG/MSF format	159	(1)
The NBRF/PIR format	160	(1)
Interconverting Formats Using PAUP*	161	(2)
Importing Various File Formats into PAUP*	161	(2)
Appendix II Printing Alignments	163	(4)
Printing to assess the quality of an alignment	163	(1)
Printing alignments for publication	164	(3)
Literature Cited	167	(2)
Index to Major Programs Discussed	169	(4)
Subject Index	173