Copyright
Disclaimer
Preface
Acknowledgements
MEGA Software Development Team
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
                Computing the Gamma Parameter
                Equal Input Model
                Jukes-Cantor Gamma distance
                Kimura distance
                Tajima Nei distance
                Tamura-Nei gamma distance
                Tamura 3-parameter distance
                Maximum Composite Likelihood (Gamma Rates)
             Heterogeneous Patterns
          Amino Acid Substitution Models
          Synonymouse and Nonsynonymous Substitution Models
       Specifying Distance Estimation Options
    Constructing Phylogenetic Trees
    Tests of Selection
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