Biological and Computational Aspects of Phylogenetic Inference and Implications for the Evolution of Life on Earth
Seminar outline:
The
seminar is open to CS, Bioinformatics, and Biology students and the
main goal is for Biologists and Computer Scientists to learn to talk to
each other, i.e., improve their interdisciplinary skills.
Locality:
The
seminar will take place at the Museum of Paleontology in Munich,
Richard-Wagner-Str. 10. Course Time: Mondays from 18:00-20:00 and a
beer nearby after the course (Start 20.04.2009 End 20.07.2009). The seminar starts at 18:00 sharp, i.e., s.t. !
Instructors:
Prof. Gert Wörheide
Dr. Alexandros Stamatakis
Participants:
Biology, Paleontology, and Bioinformatics PhD students
CS, Bioinformatics, Paleontology master/diploma students
Preliminary Schedule:
27.04 Tree Reconstruction (Alexis)
04.05 Tree Reconstruction (Alexis)
11.05 Own Research (Isabella Stoeger)
18.05 Own Research (Nico Straube)
25.05 Own Research (Fabian Schreiber)
Methods "Parallel Computation of the Likelihood Function" (Fabian Schreiber)
01.06 Pfingsten Vacations
08.06 Own Research (Sergio Vargas)
15.06 Cancelled
22.06 Paper: "Study of Birds" (Nico Straube)
Methods "Bayesian Inference" (Andre Aberer)
29.06 Paper: "Dunn et al." (Isabella Stoeger)
Papers: "Schierwater versus Herve" (Sergio Vargas)
06.07 Own research (Klementyna Karlinska)
13.07 Methods "Computing RF distances" (Safak Ökmen)
20.07 Tree Reconstruction (Alexis)
We will supplement the presentations with ad hoc lectures on phylogeny reconstruction and a bit of a RAxML tutorial.
CS Subjects & Papers:
Models:
- Maximum Likelihood
- Bayesian Inference
- Maximum Parsimony
Algorithms:
- ML and Bayesian Search Algorithms
- Computation of topological distances
- Computation of consensus tree
- Inference of Confidence Values
Parallel Computing:
- Parallelization of ML & MP
- Parallelization of Bayesian Methods
- Computer Architectures for Phylogenetic Inference
Papers:- E Mossel, E Vigoda Phylogenetic MCMC algorithms are misleading on mixtures of trees (Science 2005)
- JP Huelsenbeck et al. Potential applications and pitfalls of Bayesian inference of phylogeny
Biology Papers:
- Dunn et al. Broad phylogenomic sampling improves resolution of the animal tree of life
- SJ
Hackett et al. A phylogenomic study of birds reveals their evolutionary
history (Science 2008) (Remark: Supplement contains some interesting
notes aboutr MrBayes)
- SA Smith, MJ Donoghue Rates of molecular evolution are linked to life history in flowering plants (Science 2008)
- ORP Bininda Edmonds et al The delayed rise of present-day mammals (Nature 2007)
- Philippe et al. 2009. Phylogenomics revives traditional views on deep animal relationships, Current Biology in press
- Schierwater et al. Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern "Urmetazoon"
Hypothesis.PLoS Biology (2009) vol. 7 (1) pp. e20