Data analysis in molecular biology and evolution

1. Installation of DAMBE and a Quick Start 1 -- 1. Installation 1 -- 2. A jump start 2 -- 2. File Conversion 7 -- 1. A plethora of computer programs 8 -- 2. A Plethora of sequence formats 8 -- 3. Readseq 9 -- 4. File conversion using DAMBE 10 -- 4.1 Convert all sequences from one format to another 11 -- 4.2 Converting a subset of sequences 12 -- 4.3 Output PHYLTEST files 13 -- 3. Processing GenBank Files 17 -- 1. Genbank file format 18 -- 2. Reanding genbank files with dambe 20 -- 4. Accessing GenBank or Networked Computers 25 -- 2. Reading molecular sequences directly from GenBank 25 -- 3. Reading from and writing to another networked computer 30 -- 5. Pair-wise and Multiple Sequence Alignment 33 -- 1.1 Dot-matrix approach 33 -- 1.2 Similarity or distance method 36 -- 2. Sequence alignment using DAMBE 37 -- 2.1 Align nucleotide or amino acid sequences 37 -- 2.2 Align nucleotide sequences against amino acid sequences 38 -- 6. Factors Affecting Nucleotide Frequencies 41 -- 1.1 Frequency parameters 41 -- 1.2 Factors that might change the frequency parameters 42 -- 1.3 Frequency parameters and phylogenetic analyses 43 -- 2. Counting nucleotide and dinucleotide frequencies 44 -- 7. Case Study 1: arthropod phylogeny 49 -- 2. Obtain data from GenBank 50 -- 3. Align the sequences 53 -- 4. Data analysis 56 -- 8. Factors Affecting Codon Frequencies 59 -- 2. Generating Codon Usage Table With DAMBE 60 -- 3. DNA methylation and usage of arginine codons 64 -- 4. Transcription efficiency and codon usage bias 66 -- 5. Translational efficiency and codon usage bias 66 -- 6. Codon frequency and peptide length in ancient proteins 68 -- 9. Case Study 2: Transcription and codon usage bias 71 -- 2. Maximizing transcriptional efficiency 72 -- 3. Predictions and empirical tests 75 -- 4. An alternative explanation 85 -- 10. Case Study 3: Translation and codon usage bias 91 -- 2. Elongation model, its predictions, and empirical tests 92 -- 2.1 Adaptation of Codon Usage to tRNA Content 94 -- 2.2 Adaptation of tRNA to Codon Usage 98 -- 2.3 Evolution of tRNA in Response to Amino Acid Usage 99 -- 2.4 Translational Efficiency and Translational Accuracy 102 -- 3.1 Validity of the Model 103 -- 3.2 Translational Efficiency and Accuracy on Codon Usage Bias 104 -- 3.3 How Optimized Are the Translational Machinery? 105 -- 11. Evolution of Amino Acid Usage 107 -- 2. Amino acid usage bias 109 -- 12. Pattern of Nucleotide Substitutions 115 -- 2. Use DAMBE to document empirical substitution patterns 118 -- 2.1 Simple output 118 -- 2.2 Detailed Output 119 -- 13. Preamble to the Pattern of Codon Substitution 125 -- 2. Default substitution patterns with no selection 126 -- 14. Factors Affecting Codon Substitutions 131 -- 1.1 Rate of Codon Substitutions and its Determinants 131 -- 1.2 Models of Codon Substitution 132 -- 1.3 Expected Pattern of Nonsynonymous Substitutions 134 -- 2. Codon comparison with DAMBE 136 -- 2.1 Tracing evolutionary history 136 -- 2.2 Summary of codon substitution pattern 140 -- 2.3 Single-step Nonsynonymous Codon Substitutions 142 -- 15. Case Study 4: Transition bias 147 -- 2. Get sequence data 151 -- 3. Data analysis 152 -- 3.1 Phylogeny reconstruction 152 -- 3.2 Pair-wise comparisons between neighboring nodes 157 -- 4. Results 160 -- 16. Substitution Pattern in Amino Acid Sequences 165 -- 1. Substitution pattern from sequences in RST format 165 -- 2. Substitution pattern from all pair-wise comparisons 169 -- 17. A Statistical Digression 171 -- 2. Two Discrete Probability distributions 172 -- 2.1 Binomial Distribution and the Goodness-of-fit test 172 -- 2.2 Multinomial Distribution 174 -- 3. Simplest presentation of the maximum likelihood method 175 -- 4. Bias in the maximum likelihood method 177 --m 18. Theoretical Background of Genetic Distances 179 -- 2. Genetic Distances from Nucleotide Sequences 180 -- 2.1 JC69 and TN84 distances 181 -- 2.2 Kimura's two parameter distance 183 -- 2.3 F84 distance 184 -- 2.4 TN93 distance 185 -- 2.5 Lake's paralinear distance 186 -- 3. Distances based on codon sequences 187 -- 3.1 Empirical counting approach 188 -- 3.2 Codon-based maximum likelihood method 190 -- 4. Distances based on amino acid sequences 191 -- 5. Genetic Distances from Allele Frequencies 192 -- 5.1 Nei's genetic distance 193 -- 5.2 Cavalli-Sforza's chord measure 195 -- 5.3 Reynolds, Weir, and Cockerham's genetic distance 195 -- 19. Molecular Phylogenetics: Concepts and Practice 197 -- 1. Molecular clock and its calibration 198 -- 1.1 Calibrating a molecular clock 199 -- 1.2 Complications in calibrating a molecular clock 201 -- 2. Common approaches in molecular phylogenetics 204 -- 2.1 Distance methods 204 -- 2.2 Maximum parsimony method 212 -- 2.3 Maximum likelihood method 213 -- 2.4 Reconstructing Ancestral Sequences 219 -- 20. Testing the Molecular Clock Hypothesis 223 -- 1. T-test 224 -- 2. Likelihood ratio test 225 -- 3. Test the molecular clock hypothesis 228 -- 21. Testing Phylogenetic Hypotheses 231 -- 1. Basic statistical concepts 232 -- 2. Testing phylogenetic hypotheses with the distance method 234 -- 2.1 Rationale 234 -- 2.2 Test alternative phylogenetic hypotheses: distance methods 236 -- 3. Testing phylogenetic hypotheses with the parsimony method 239 -- 4. Testing phylogenetic hypotheses with the likelihood method 241 -- 5. Resampling methods 244 -- 22. Fitting Probability Distributions 247 -- 1.1 Poisson distribution 248 -- 1.2 Negative binomial distribution 250 -- 1.3 Gamma distribution 252 -- 1.4 Some general guidelines for fitting statistical distributions 255 -- 2. Fitting discrete Distributions with DAMBE 256 -- 3. Estimating the shape parameter of the gamma distribution 259