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Phylogenetic data analysis, spring 2009

Lecturer

dos. Sirkka-Liisa Varvio

Scope and type

6-9 cu, advanced studies

Lectures

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-exercises

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

 

Examination

  • 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

  • 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.
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