The Exelixis Lab

Enabling Research in Evolutionary Biology

bioinformatics module slides

bioinformatics class winter 2022/23

bioinformatics class winter 2021/22

Slides and videos will become available on-line soon, to get a first impression please have a look at the 2020/21 slides from last winter as there will not be any major changes.

bioinformatics class winter 2020/21

bioinformatics class winter 2019/20

bioinformatics class winter 2018/19

bioinformatics class winter 2017/18

bioinformatics class winter 2016/17

bioinformatics class winter 2015/16

bioinformatics class winter 2014/15

bioinformatics class summer 2014

bioinformatics class winter 2012/13

lecture 1
lecture 2
lecture 3 some more biological stuff + review of the knowledge test (Alexis)
Instruction Level Parallelism: A nice outline of Tomasulo's algorithm for out-of-order execution in pipelines can be found in these slides by D.A. Patterson at Berkeley.
He has also written a very nice book about computer architectures with J.L. Hennessy: "Computer Architecture - A Quantitative Approach."
lecture 4
lecture 4 a: Sequencing insect transcriptomes & review of the knowledge test
lecture 4 b: pair-wise sequence alignment (Solon & Alexis)
lecture 5: Blast & Genome assembly (Solon & Alexis)
lecture 6: Suffix trees (Tomas & Alexis)
lecture 7: Multiple Sequence Alignment (Alexis)
lecture 8: Introduction to Phylogenetics (Alexis)
lecture 9: Phylogenetic Inference Algorithms (Alexis)
lecture 10:
lecture 10 a: Phylogenetic Search Operators (Alexis)
lecture 10 b: The Maximum Likelihood Model in Phylogenetics (Kassian)
A textual description of the maximum likelihood model can also be found on pages 20 to 31 of Alexis PhD thesis
Kassian's whiteboard drawings:
lecture 11: Advanced Maximum Likelihood Models & Parallel Computing in Phylogenetics (Alexis)
lecture 12  (handout version): Discrete operations on phylogenetic trees (Andre)
lecture 13, lecture 13 (blackboard drawings & equations) : Introduction to population genetics (Pavlos)
lecture 14: The Coalescent (Pavlos)
lecture 15: Wrap-up and exam preparation (Alexis)