Unit1
Unit 1: PHYLOGENETIC TREES
8 hrsTypes- topological differences- tree building methods- Distance methods- UPGMA- LS methods-minimum evaluation methods- NJ methods- phylogenetic reconstruction.
Syllabus
5 units · 40 lecture hoursUnit2
Unit 2: METHODS
8 hrsMaximum parsimony methods- Strategies of searching for MP trees- consensus trees- branch length estimation - weighted parsimony- MP methods for protein data- Maximum likelihood methods.
Unit3
Unit 3: STATISTICAL APPROACH
8 hrsOptimization principle and topological errors- interior branch tests- bootstrap tests- Tests of topological differences-advantages and disadvantages-molecular clocks and linearized trees.
Unit4
Unit 4: ANCESTRAL SEQUENCES
8 hrsInferences of ancestral sequences parsimony and Bayesian approaches- synonymous and non-synonymous substitutions- convergent and parallel evolution.
Unit5
Unit 5: EVOLUTION
8 hrsMolecular basis of evolution- synonymous and non-synonymous mutations-genetic polymorphism and evolution- Population trees from genetic marker. Dr. A.P.J. Abdul Kalam Technical University, Lucknow, Uttar Pradesh
Course Outcomes (COs)
After completion of the course student will be able to:
- CO1Understand phylogenetic trees, their types, topological differences, and tree-building methods (UPGMA, LS, NJ, reconstruction).K2
- CO2Apply maximum parsimony and maximum likelihood methods for consensus trees, branch length estimation, and protein data analysis.K3
- CO3Explain statistical approaches in phylogenetics, including optimization principles, bootstrap tests, molecular clocks, and linearized trees.K2
- CO4Apply parsimony and Bayesian approaches to infer ancestral sequences and explain synonymous/non-synonymous substitutions, convergent and parallel evolution.K3
- CO5Explain the molecular basis of evolution, genetic polymorphism, and population trees derived from genetic markers.K2
TEXT BOOKS
- / REFERENCES
- Bruce S. Lieberman, “Phylogenetics: Theory and Practice of Phylogenetic Systematics”, Wiley-Blackwell, second edition, 2011.
- Masatoshi Nei, “Molecular Evolution and Phylogenetics”, Oxford University Press, 2000.
- David W Mount, “Bioinformatics- Sequence and genome analysis”, Cold Spring Harbor Laboratory Press, second edition, 2004.
- Roderick D.M. Page, Dr Edward C. Holmes, “Molecular Evolution: A Phylogenetic Approach”, Blackwell Publishing, 1998.
- Jin Xiong, “Essential Bioinformatics”, Cambridge University Press, 2006. Dr. A.P.J. Abdul Kalam Technical University, Lucknow, Uttar Pradesh
Official AKTU syllabus
This subject is on page 13, 14, 15 of the original AKTU PDF.