Disclaimer
Preface
Acknowledgements
MEGA Software Development Team
Copyright
Citing MEGA in Publications
Part I: Getting Started
Part II: Assembling Data for Analysis
Part III: Input Data Types and File Format
Part IV: Evolutionary Analysis
    Computing Basic Statistical Quantities for Sequence Data
    Computing Evolutionary Distances
       Distance Models
          Introduction
          Nucleotide Substitution Models
             No. of differences
             p-distance
             Jukes-Cantor distance
             Tajima-Nei distance
             Kimura 2-parameter distance
             Tamura 3-parameter distance
             Tamura-Nei distance
             Maximum Composite Likelihood Method
             Gamma Distances
             Heterogeneous Patterns
                Tajima Nei Distance (Heterogeneous)
                Tamura 3 parameter (Heterogeneous)
                Tamura-Nei distance (Heterogeneous)
                Maximum Composite Likelihood (Heterogeneous Patterns)
                Gamma Rates
          Amino Acid Substitution Models
          Synonymouse and Nonsynonymous Substitution Models
       Specifying Distance Estimation Options
    Constructing Phylogenetic Trees
    Constructing Time Trees
    Handling Missing Data and Alignment Gaps
    Tests of Selection
    Exploring the impact of nsSNVs
    Identifying Gene Duplications
Part V: Visualizing and Exploring Data and Results
Appendix A: Frequently Asked Questions
Appendix B: Main Menu Items and Dialogs Reference
Appendix C: Error Messages
Glossary
References