Universität Wien
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053522 VU Bioinformatics for phylogeny and evolutionary tree reconstruction (2024W)

3.00 ECTS (2.00 SWS), SPL 5 - Informatik und Wirtschaftsinformatik
Continuous assessment of course work
Moodle

Registration/Deregistration

Note: The time of your registration within the registration period has no effect on the allocation of places (no first come, first served).

Details

max. 25 participants
Language: English

Lecturers

Classes (iCal) - next class is marked with N

IMPORTANT: Due to conflicting time slots with the VU Statistical methods in bioinformatics, this course was postponed from Thursday mornings to the afternoon. (Locations and dates remained the same.)

  • Thursday 03.10. 13:00 - 15:00 STB/Seminarraum Strukturchemie Campus Vienna Biocenter 5, 1030 Wien (Kickoff Class)
  • Thursday 10.10. 13:00 - 15:00 STB/Seminarraum Strukturchemie Campus Vienna Biocenter 5, 1030 Wien
  • Thursday 17.10. 13:00 - 15:00 STB/Seminarraum Strukturchemie Campus Vienna Biocenter 5, 1030 Wien
  • Thursday 24.10. 13:00 - 15:00 STB/Seminarraum Strukturchemie Campus Vienna Biocenter 5, 1030 Wien
  • Thursday 31.10. 13:00 - 15:00 STB/Seminarraum Strukturchemie Campus Vienna Biocenter 5, 1030 Wien
  • Thursday 07.11. 13:00 - 15:00 STB/Seminarraum Strukturchemie Campus Vienna Biocenter 5, 1030 Wien
  • Thursday 14.11. 13:00 - 15:00 STB/Seminarraum Strukturchemie Campus Vienna Biocenter 5, 1030 Wien
  • Thursday 21.11. 13:00 - 15:00 STB/Seminarraum Strukturchemie Campus Vienna Biocenter 5, 1030 Wien
  • Thursday 28.11. 13:00 - 15:00 STB/Seminarraum Strukturchemie Campus Vienna Biocenter 5, 1030 Wien
  • Thursday 05.12. 13:00 - 15:00 STB/Seminarraum Strukturchemie Campus Vienna Biocenter 5, 1030 Wien
  • Thursday 12.12. 13:00 - 15:00 STB/Seminarraum Strukturchemie Campus Vienna Biocenter 5, 1030 Wien
  • Thursday 09.01. 13:00 - 15:00 STB/Seminarraum Strukturchemie Campus Vienna Biocenter 5, 1030 Wien
  • Thursday 16.01. 13:00 - 15:00 STB/Seminarraum Strukturchemie Campus Vienna Biocenter 5, 1030 Wien
  • Thursday 23.01. 13:00 - 15:00 STB/Seminarraum Strukturchemie Campus Vienna Biocenter 5, 1030 Wien
  • Thursday 30.01. 13:00 - 15:00 STB/Seminarraum Strukturchemie Campus Vienna Biocenter 5, 1030 Wien

Information

Aims, contents and method of the course

Overview: Phylogenetics is the research field that deals with the reconstructions of evolutionary relationships of biomolecules like DNA and proteins, organisms or viruses. It is, thus, fundamental to many biological analysis such as epidemiology surveillance.
a. Aims: Understanding of the bioinformatics concepts and methods of phylogenetics and evolutionary tree reconstruction in theory and practice;
b. Content: The course aims at giving a broad overview covering topics like historical background; theoretical basics and definitions; different approaches like maximum parsimony, distance methods, maximum likelihood and Bayesian and associated algorithms; tree search and tree rearrangements; models of sequence evolution and model selection; summarizing trees and branch support; tree topology testing; tracing phylogenetic signal and noise; phylogenomics, supertrees and partition models; ancestral state reconstruction, phylogeography.
c. Methods: Lectures, graded exercises (submitted via Moodle) and, finally, the course includes two practical units applying phylogenetic software.

Assessment and permitted materials

a. Type of assessment: To all lectures and the two practical units exercise sheets have to be solved and submitted (via Moodle). For each exercise sheet the same amount of points can be achieved. To pass the course one has to obtain at least 50% of the possible sum of points.
b. Permitted material: Solutions have to be written by oneself. Copy-and-paste from other sources is not allowed. References to all third-party material have to be given.

Minimum requirements and assessment criteria

a. Minimum requirements: To pass the course one has to obtain at least 50% of the possible weighted sum of points. The obtained percentage of the points determines the actual grade.
b. Assessment criteria: The following obtained percentages correspond to the following grades:
>=87.5%: grade 1 (very good)
<87.5%: grade 2 (good)
<75.0%: grade 3 (satisfactory)
<62.5%: grade 4 (sufficient)
<50.0%: grade 5 (insufficient)

Examination topics

Relevant is all content of the lectures and exercises.

Reading list

Possible textbooks and additional references will be given during the lectures.

Association in the course directory

Module: BIOINF06

Last modified: We 11.09.2024 11:25