Phylogenetic data analysis, spring 2009

6-9 cu, advanced studies

Period IV, Monday 15.30-17 in room D123, Friday 12-14 in room BK106 (all in Exactum).

Mon Fri	Lecture slides.pdf	Other material
week 1	Introduction.pdf modelling sequence evolution I..pdf	http://evolution.genetics.washington.edu/phylip/software.html
week 2	distance matrix methods..pdf Phylonews I..pdf Maximum parsimony..pdf	http://www.megasoftware.net/
week 3	Phylonews II.pdf maximum likelihood.pdf
week 4	Modelling sequence evolution II.pdf Frequentist and Bayesian tree confidence and credibility.pdf Phylonews III.pdf
week 5	Bayesian phylogeny inference.pdf	Huelsenbeck_Ronquist.pdf http://mrbayes.csit.fsu.edu/, MrBayes Manual.pdf,MrBayes Commands.pdf,

week 6	Evolutionary_rates.pdf Phylogenies of species and genes	http://abacus.gene.ucl.ac.uk/software/paml.html

home-exercise1	(see last page of "Modelling sequence evolution I.pdf"
home-exercise2	(see last page of "Distance matrix methods.pdf"
Home-exercise3.pdf	home_exe3_data.txt
home-exercise4.pdf	Bootstrap Posterior Prob1.pdf,Bootstrap Posterior Prob2.pdf
Evolutionary rates.pdf	Home_exe5.txt, Home_exe5.nex, Bayesian_positive.pdf

Monday, May 4. 16-19 in room B123. In addition to lecture material there will be one question either from this Article1.pdf , or from this Article2.pdf. The question is: Write a short essay, ~2 pages, on the basis of ArticleX. So, you can prepare these short essays in advance (and bring them with you within your mind, not written in paper). You are not supposed to understand everything in the papers (it is impossible !), try to understand something.
Passing the course worth 6 cu is based on the examination and home-exercises. Examination gives you 5 cu and home-exercises 1 cu.

Own project.pdf is worth 2 cu.
Literature survey: You can get one more cu by a short (~2-3 pages report) literature survey concerning phylogenetic inference, either practical or theoretical studies (or both).
In total you can get 9 cu from the course.