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This is an introduction for biologists to DAMBE, a proprietary, user-friendly computer program for molecular data analysis. The combination of this book and software will allow biologists not only to understand the rationale behind a variety of computational tools in molecular biology and evolution, but also to gain instant access to these tools for use in their laboratories.
Acknowledgements. Preface. 1. Installation of DAMBE and a Quick Start. 2. File Conversion. 3. Processing GenBank Files. 4. Accessing GenBank or Networked Computers. 5. Pair-wise and Multiple Sequence Alignment. 6. Factors Affecting Nucleotide Frequencies. 7. Case Study 1: arthropod phylogeny. 8. Factors Affecting Codon Frequencies. 9. Case Study 2: Transcription and codon usage bias. 10. Case Study 3: Translation and codon usage bias. 11. Evolution of Amino Acid Usage. 12. Pattern of Nucleotide Substitutions. 13. Preamble to the Pattern of Codon Substitution. 14. Factors Affecting Codon Substitutions. 15. Case Study 4: Transition bias. 16. Substitution Pattern in Amino Acid Sequences. 17. A Statistical Digression. 18. Theoretical Background of Genetic Distances. 19. Molecular Phylogenetics: Concepts and Practice. 20. Testing the Molecular Clock Hypothesis. 21. Testing Phylogenetic Hypotheses. 22. Fitting Probability Distributions. Literature Cited. Index.