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Default Sathyabama Institute of Science and Technology M.Sc - Bioinformatics and Datascience SBIA7402 Phylogenetic analysis Syllabus

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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