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Phylogenetic Trees Made Easy 2nd Revised edition [Mīkstie vāki]

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  • Formāts: Paperback / softback, 238 pages, height x width: 235x178 mm, weight: 408 g, 155 illustrations
  • Izdošanas datums: 01-Jan-2004
  • Izdevniecība: Sinauer Associates Inc.,U.S.
  • ISBN-10: 0878933123
  • ISBN-13: 9780878933129
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  • Formāts: Paperback / softback, 238 pages, height x width: 235x178 mm, weight: 408 g, 155 illustrations
  • Izdošanas datums: 01-Jan-2004
  • Izdevniecība: Sinauer Associates Inc.,U.S.
  • ISBN-10: 0878933123
  • ISBN-13: 9780878933129
Citas grāmatas par šo tēmu:
Phylogenetic Trees Made Easy helps beginners 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 may be familiar with phylogenetic theory but are 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 these sequences from databases, creating multiple alignments and using several different methods to construct trees. Key changes to the Second Edition include: content and screen shots have been updated to reflect current software versions new "Advanced Topics" to extend understanding detailed discussion of PAUP as well as inclusion of PHYLIP as an alternative. Every copy of the Second Edition also includes a CD with current Windows and Macintosh beta versions of PAUP .
Introduction: Read Me First 1(1)
A Brief Overview of the Second Edition
2(1)
Time-Limited Copy of the PAUP*4.0 Program
3(1)
Learn More about the Principles
4(1)
Computer Programs Discussed and Where to Obtain Them
4(3)
ClustalX
5(1)
Tree View
5(1)
PAUP*
5(1)
PHYLIP (PHYLogeny Inference Package)
6(1)
Tree-Puzzle
6(1)
MrBayes
7(1)
CodonAlign
7(1)
Other Programs
7(1)
Files and Utilities on the ``Phylogenetics Made Easy'' Website and CD
7(1)
Some Conventions Used in This Book
8(1)
Tutorial: Create a Tree!
9(52)
Why Create Phylogenetic Trees?
9(1)
Obtaining Related Sequences by a BLAST Search
10(13)
Step 1: Go to the BLAST Website
11(2)
Step 2: Use BLAST to Search for Sequences Related to Your Sequence
13(1)
Step 3: Decide Which Related Sequences to Include on Your Tree
14(6)
Downloading the Selected Sequences
20(3)
Creating the Multiple Alignment
23(17)
Creating the Input File
24(2)
Getting the Data into ClustalX
26(1)
Some General Comments about Creating Alignments
27(1)
Setting the Alignment Parameters
27(5)
Creating the Alignment
32(1)
Refining and Improving the Alignment
33(5)
Aligning New Sequences to an Existing Alignment, or Aligning Two Existing Alignments
38(2)
Phylogenetic Analysis
40(2)
Exactly What Is a Phylogenetic Tree?
41(1)
Methods for Constructing Phylogenies
41(1)
Learn More About Phylogenetic Trees
42(10)
Using ClustalX to Create a Neighbor Joining Tree
46(1)
Drawing the Tree Using Tree View
47(1)
Tree Formats: Different Appearances of the Same Tree
47(3)
Bootstrapping a Tree
50(2)
Learn More About Estimating The Reliability of Phylogenetic Trees
52(4)
Placing the Root of a Tree
53(3)
Learng More About Rooting Phylogenetic Trees
56(4)
Printing and Saving the Tree
59(1)
Summary
60(1)
Basic Elements in Creating and Presenting Trees
61(96)
Selecting Homologs: What Sequences Can Be Put on a Single Tree?
61(3)
Fine-Tuning Alignments
64(4)
Major Methods for Creating Trees
68(2)
Which Method Should You Use?
68(1)
Distance versus Character-Based Methods
69(1)
Learn More About Tree-Searching Methods
70(4)
Learn More About Distance Methods
74(2)
Data Files Used to Illustrate Methods
76(1)
Using PAUP* to Create Trees
76(18)
Opening the Input File
77(3)
Creating Neighbor-Joining Trees Using PAUP*
80(12)
Creating Parsimony Trees Using PAUP*
92(2)
Learn More About Parsimony
94(10)
Creating a Consensus Tree Using PAUP*
100(2)
Creating Maximum Likelihood DNA Trees Using PAUP*
102(2)
Learn More About Maximum Likelihood
104(6)
Learn More About Evolutionary Methods
110(4)
Creating Maximum-Likelihood Protein Trees Using Tree-Puzzle
114(4)
Creating Bayesian Trees Using MrBayes
118(2)
Creating the Execution File
119(1)
Learn More About Bayesian Analysis
120(15)
What the Statements in the Example MrBayes Block Do
123(5)
Interpreting MrBayes Results
128(2)
Sample Blocks for MrBayes
130(2)
Getting Help
132(3)
Presenting and Printing Your Trees
135(12)
Opening Tree Files in PAUP*
135(4)
To Root or Not to Root?
139(8)
Choosing What Form of a Tree to Publish
147(1)
Making a Tree Pretty: Not Just a Cosmetic Matter
148(4)
DNA Phylogeny or Protein Phylogeny: Which Is Better?
152(5)
Using CodonAlign 2.0
154(3)
Advanced Elements in Constructing Trees
157(22)
Reconstructing Ancestral DNA Sequences
157(10)
Ancestral Sequences for Parsimony and Maximum Likelihood Trees Using PAUP*
158(3)
Ancestral Sequences for Parsimony using PHYLIP
161(6)
Using Protein Structure Information to Construct Very Deep Phylogenies
167(6)
Analyzing Trees for Evidence of Adaptive Evolution by Detecting Positive Selection in a Phylogeny
173(6)
Using Alternative Software to Construct and Present Trees
179(14)
Using PAUP* with Windows or Unix
179(8)
Opening and Viewing Files
180(2)
Using PAUP Blocks
182(3)
Bootstrapping
185(2)
Using PHYLIP
187(6)
General Features of PHYLIP Programs
188(1)
Parsimony Trees
189(1)
Consensus Trees
190(1)
Neighbor-Joining Trees
190(1)
Maximum Likelihood Trees
191(1)
Bootstrapping
191(2)
Appendix I File Formats and Their Interconversion
193(12)
Formats Used by Programs Discussed in this Book
193(6)
The FASTA Format
193(1)
The Clustal Format
194(1)
The Nexus Format
195(2)
PHYLIP 3.x
197(2)
Other File Formats
199(2)
The GCG/MSF Format and PileUp
199(1)
The NBRF/PIR format
200(1)
Interconverting Formats Using PAUP*
201(2)
Importing Various File Formats into PAUP*
201(1)
Exporting Various File Formats from PAUP*
202(1)
Interconverting Interleaved and Sequential Formatted PHYLIP Files
203(2)
Appendix II Printing Alignments
205(2)
Printing to Assess the Quality of the Alignment
205(1)
Printing Alignments for Publication
206(1)
Literature Cited 207(2)
Index to Major Programs Discussed 209(6)
Subject Index 215
BARRY G. HALL, Emeritus, University of Rochester, USA.