Contents

Cover

Preface

1. Getting Started

1.1 Hardware and Software
1.2 Installing MEGA
1.3 Running MEGA
1.4 README File
1.5 Technical Support and Updates
1.6 For Classroom Teaching
1.7 Source Code Availability

2. Input Data and Formats

2.1 MEGA Format

2.1.1 Key Words
2.1.2 OTU Labels

2.2 Sequence Input Formats
2.3 Distance Input Formats
2.4 Editing Sequence Data
2.5 Editing Distance Data

3. Basic Sequence Statistics

3.1 Nucleotide and Amino Acid Compositions
3.2 Codon Usage
3.3 Nucleotide Pair Frequencies
3.4 Alignment Gap Frequencies
3.5 Variable Regions of Sequences

4. Distance Estimation

4.1 Nucleotide Substitutions
4.2 Synonymous and Nonsynonymous Substitutions
4.3 Amino Acid Substitutions
4.4 Guidelines for Choosing Distance Measures
4.5 Alignment Gaps and Sites with Missing Information

5. Phylogenetic Inference

5.1 Phylogenetic Trees
5.2 Tree-Building Methods
5.3 UPGMA
5.4 Neighbor-Joining (NJ) Method

5.5 Maximum Parsimony (MP) Method

5.5.1 Branch-and-Bound Search
5.5.2 Heuristic Search
5.5.3 Alignment Gaps and Sites with Missing Information
5.5.4 Consensus Trees

5.6 Statistical Tests of a Tree Obtained

5.6.1 NJ Trees
5.6.2 UPGMA Trees
5.6.3 MP Trees
5.6.4 Condensed Trees
5.6.5 General Comments on Statistical Tests

6. User-Interface

6.1 Screen

6.1.1 Menubar, Desktop, and Status Line
6.1.2 Hot-Keys and Short-Cuts

6.2 Windows and Dialog Boxes
6.3 File Name Dialog Box
6.4 Context-Sensitive Help Box
6.5 Text-File Browser
6.6 Text-File Editor
6.7 Sequence Data Presentation
6.8 Phylogenetic-Tree Editor
6.9 Printing Trees

7. Walk through MEGA

7.1 Constructing Trees from Distance Data
7.2 Computing Statistical Quantities for Nucleotide Sequences
7.3 Estimating Evolutionary Distances from Nucleotide Sequences
7.4 Constructing Trees and Selecting OTUS from Nucleotide Sequences
7.5 Tests of the Reliability of a Tree Obtained
7.6 Test of Positive Selection

8. Command Reference

MEGA

About MEGA

Reference

Calculator

Calendar

Thank You

Using Help

File

Browse

Edit

Change Dir

DOS Shell

Exit MEGA

Data

Open Data

Close Data

Select OTUs

Select Mode

Select Sites/Codons

Select Outgroups

Edit OTU Labels

Restore OTU Labels

Data Presentation

Distance

Nucleotide

Syn-Nonsynonymous

Amino Acid

Cenetic Code Table

Compute Distances

Phylogeny

UPGMA

Neighbor-Joining

Maximum Parsimony

Construct Tree(s)

Bootstrap Test

Standard Error Test

Window

Resize/Move

Zoom

Tile

Cascade

Next

Previous

Close

9. Error Messages

References

Appendix A: Functions in MEGA

Appendix B: Common Questions and Answers

Appendix C: Mathematical Notations and Abbreviations

Appendix D: Printers Supported

Appendix E: Other Computer Programs Available