Data Analysis in Molecular Biology and Evolution

Dr. Xuhua Xia is affiliated with the University of Hong Kong and specializes in bioinformatics.

Installation of DAMBE and a Quick Start.- File Conversion.- Processing GenBank Files.- Accessing GenBank or Other Networked Computers.- Pair-wise and Multiple Sequence Alignment.- Factors Affecting Nucleotide and Di-Nucleotide Frequencies.- Case Study 1.- Factors Affecting Codon Frequencies and Codon Usage Bias.- Case Study 2.- Case Study 3.- Evolution of Amino Acid Usage.- Pattern of Nucleotide Substitutions.- Preamble to the Pattern of Codon Substitution.- Factors Affecting Codon Substitutions.- Case Study 4.- Substitution Pattern in Amino Acid Sequences.- A Statistical Digression.- Theoretical Background of Genetic Distances.- Molecular Phylogenetics: Concepts and Practice.- Testing the Molecular Clock Hypothesis.- Testing Phylogenetic Hypotheses.- Fitting Probability Distributions To Substitutions Over Sites.