1. SylabUZ
2. Wydział Nauk Biologicznych
3. semestr zimowy 2019/2020
4. WNB - oferta ERASMUS - Program Erasmus
5. Techniques of phylogenesis reconstruction

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Techniques of phylogenesis reconstruction - opis przedmiotu

Cel przedmiotu

Acquiring knowledge about the characteristics and construction of phylogenetic trees and their important parameters. Understanding the importance of phylogenetic tree topology, generation of clades and nodes. Understanding the purpose of various types of trees (filograms, cladograms, unrooted trees). Acquiring knowledge about algorithms used to construct phylogenetic trees. Acquiring the ability to construct molecular phylogenetic trees based on different computational algorithms. Acquiring the ability to interpret results and retrieve information resulting from phylogenetic trees.

Wymagania wstępne

Zapisz zmiany

Computer and Internet skills.

Zakres tematyczny

Stages of phylogenetic trees construction. Calculation of evolutionary distances. The main characteristics of phylogenetic trees. Rooted and unrooted trees. Various forms of graphical representation of phylogenetic trees - cladograms, filograms and unrooted trees. Comparing phylogenetic trees. Newick format. Theoretical basis of algorithms used to generate phylogenetic trees. The Neighbor Joining, Maximum Parsimony, Maximum Likelihood, Bayesian Inference methods - characteristics and application. Programs for generating phylogenetic trees. Creating consensus phylogenetic trees. Comparison of phylogenetic trees generated on the basis of analysis of nucleotide sequences and corresponding amino-acid sequences. Selected phylogenetic analyzes (e.g. using the Python program). Practical exercises of constructing phylogenetic trees and reconstructing phylogenesis using selected methods of artificial intelligence.

Metody kształcenia

Lecture with multimedia presentations and the use of online databases and specialized bioinformatics software for the construction, visualization and analysis of molecular phylogenetic trees. Laboratory - selected phylogenetic analyzes: construction of phylogenetic trees, reconstruction of phylogenesis using selected methods of artificial intelligence.

Efekty uczenia się i metody weryfikacji osiągania efektów uczenia się

Opis efektu	Symbole efektów	Metody weryfikacji	Forma zajęć

Warunki zaliczenia

Lecture - written colloquium consisting of 5 questions. The correct answers to at least 3 questions (60%) are required to get the pass mark credit. Laboratory - the condition for passing is to obtain positive grades from all laboratory exercises planned for implementation as part of the laboratory program.

Literatura podstawowa

1. Bioinformatics and Molecular Evolution, Paul G. Higgs, Teresa K. Attwood, Wiley-Blackwell, 2005.

2. Phylogenetic Trees Made Easy, Barry G. Hall, Oxford University Press, 2017.

Literatura uzupełniająca

Fundamentals of Molecular Evolution, Dan Graur, Wen-Hsiung Li, 2000.

Uwagi

Zmodyfikowane przez dr hab. inż. Andrzej Kasperski, prof. UZ (ostatnia modyfikacja: 30-04-2019 17:42)