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Sathyabama Institute of Science and Technology M.Sc - Bioinformatics and Datascience SBIA7402 Phylogenetic analysis Syllabus SATHYABAMA INSTITUTE OF SCIENCE AND TECHNOLOGY SCHOOL OF BIO AND CHEMICAL ENGINEERING SBIA7402 PHYLOGENETIC ANALYSIS L T P Credits Total Marks 3 0 0 3 100 UNIT I MOLECULAR BASIS OF EVOLUTION Molecular basis of evolution - Evolutionary tree of life - Mechanisms of evolution - Mutation and codon age. Evolutionary changes in amino acid sequences - Differences and proportion - Amino acid substitution matrix - Mutation rate and substitution rate. Evolutionary changes in DNA sequences - Nucleotide differences - Estimation of number of nucleotide substitutions - Gamma distances - Numerical estimation - alignment - Handling of sequence gaps in the estimation of evolutionary distances. Software tools for Sequence alignment - ClustalW, BioEdit, Hmmer, T-coffee, MAFFT, MultiAlign. UNIT II PHYLOGENETIC TREES Synonymous and Non-Synonymous Nucleotide substitutions - Evolutionary pathway methods - Methods based on Kimura’s 2 - Jones-Taylor-Thornton (JTT) model, Parameter Models - Nucleotide substations at different codon positions - Likelihood methods with codon substitution models. Phylogenetic trees - Types of phylogenetic trees - Topological differences - Tree building methods. Horizontal gene transfer. UNIT III PHYLOGENETIC TREE BUILDING METHODS Phylogenetic Inference -Tree building methods - Distance methods - UPGMA - Minimum Evolution method - Neighbor Joining method - Distance measures to be used for phylogenetic reconstruction - Maximum Parsimony methods - Finding MP trees - Strategies for searching - Consensus trees - Estimation of branch lengths - Weighted parsimony - Maximum Likelihood methods - Compuational procedure - Models - Protein likelihood - Theoretical foundation - Parameter estimation UNIT IV OPTIMIZATION PRINCIPLES Accuracies and Statistical tests - Optimization principle and topological errors - Interior branch tests - Bootstrapping and Jack-knifing. Advantages and disadvantages of different tree building methods - Molecular clocks - Hypothesis - Relative rate tests - Linearized trees - Ancestral nucleotide and amino acid sequences - Bayesian approach - convergent and parallel evolution. UNIT V APPLICATIONS IN PHYLOGENETICS Genetic Polymorphism and Evolution - Evolutionary significance - analysis of allele frequency data - DNA polymorphism - Statistical tests - Population trees fr om genetic markers - Analysis of RAPD data - Software Tools - TreeView - MrBayes, PAUP, PHYLIP, Spectronet, HYPHY, Dendroscope, FigTree, ModelTest, Mesquite and MEGA. Learning Outcomes CO 1: Describe evolutionary process at the molecular level CO 2: Apply molecular methods to study genetic variation within and between species CO 3: Explain and justify different models of sequence evolution CO 4: Explain and evaluate different phylogenetic optimality criteria, and select adequate criterion to solve a given problem CO 5: Sketch and apply the process to do and evaluate a phylogenetic analysis, and explain the different steps CO 6: Select and apply, for the problem area, existing software on a given biological problem TEXT / REFERENCE BOOKS 1. Joseph Felsenstein, Inferring Phylogenies,1st edition Sinauer Associates Inc, 2004 2. Baxevanis and Oulette, Bioinformatics Practical guide, Wiley, 2005 3. Durbin, Biological sequence Analysis, 1st Edition, 1998 4. David Mount, Bioinformatics: Sequence and Genome Analysis, 2nd Edition, CSHL press 2004 5. Masatoshi Nei, Molecular Evolution and Phylogenetics, Oxford University press, 200 END SEMESTER EXAM QUESTION PAPER PATTERN Max. Marks: 100 Exam Duration: 3 Hrs. PART A: 6 Questions for 5 Marks each –without choice 30 Marks PART B: 2 Questions from each unit with internal choice, each carrying 14 marks 70 Marks SBIA7 |
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