Last modified by varvio@helsinki_fi on 2024/03/27 10:00
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1 = (% style="color: rgb(0,102,102);" %)Phylogenetic data analysis, spring 2009(%%) =
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3 === (% style="color: rgb(0,102,102);" %)Lecturer(%%) ===
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5 [[dos. Sirkka-Liisa Varvio>>doc:mathstatHenkilokunta.Varvio, Sirkka-Liisa]]
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7 === (% style="color: rgb(0,102,102);" %)Scope and type(%%) ===
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9 6-9 cu, advanced studies
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11 === (% style="color: rgb(0,102,102);" %)Lectures(%%) ===
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13 Period IV, **Monday 15.30-17** in room D123, **Friday 12-14** in room BK106 (all in Exactum).
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16 Mon
17 Fri\\
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19 Lecture slides.pdf\\
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21 Other material\\
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24 week 1
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26 Introduction.pdf
27 [[modelling sequence evolution I..pdf>>attach:Modelling sequence evolution I.pdf]]\\
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29 [[http:~~/~~/evolution.genetics.washington.edu/phylip/software.html>>url:http://evolution.genetics.washington.edu/phylip/software.html||shape="rect"]]
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32 week 2\\
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34 [[distance matrix methods..pdf>>attach:Distance matrix methods.pdf]]
35 [[Phylonews I..pdf>>attach:Phylonews I.pdf]]
36 [[Maximum parsimony..pdf>>attach:Maximum parsimony.pdf]]
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38 [[http:~~/~~/www.megasoftware.net/>>url:http://www.megasoftware.net/||shape="rect"]]
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41 week 3\\
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43 Phylonews II.pdf
44 [[attach:maximum likelihood.pdf]]\\
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49 week 4\\
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51 [[attach:Modelling sequence evolution II.pdf]]
52 [[attach:Frequentist and Bayesian tree confidence and credibility.pdf]]
53 Phylonews III.pdf
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59 week 5\\
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61 [[doc:mathstatKurssit.Bayesian phylogeny inference\.pdf]]
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64 [[doc:mathstatKurssit.Huelsenbeck_Ronquist\.pdf]]
65 [[http:~~/~~/mrbayes.csit.fsu.edu/>>url:http://mrbayes.csit.fsu.edu/||shape="rect"]],
66 [[attach:MrBayes Manual.pdf]],[[doc:mathstatKurssit.MrBayes Commands\.pdf]],
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76 week 6\\
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78 [[doc:mathstatKurssit.Evolutionary_rates\.pdf]]
79 Phylogenies of species and genes\\
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81 [[http:~~/~~/abacus.gene.ucl.ac.uk/software/paml.html>>url:http://abacus.gene.ucl.ac.uk/software/paml.html||shape="rect"]]
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84 === (% style="color: rgb(0,102,102);" %)Home-exercises(%%) ===
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87 home-exercise1\\
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89 (see last page of "Modelling sequence evolution I.pdf"\\
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92 home-exercise2\\
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94 (see last page of "Distance matrix methods.pdf"\\
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97 [[doc:mathstatKurssit.Home-exercise3\.pdf]]\\
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99 [[doc:mathstatKurssit.home_exe3_data\.txt]]
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102 [[doc:mathstatKurssit.home-exercise4\.pdf]]\\
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104 [[doc:mathstatKurssit.Bootstrap Posterior Prob1\.pdf]],[[doc:mathstatKurssit.Bootstrap Posterior Prob2\.pdf]]
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107 [[doc:mathstatKurssit.Evolutionary rates\.pdf]]
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109 [[doc:mathstatKurssit.Home_exe5\.txt]], [[doc:mathstatKurssit.Home_exe5\.nex]], [[doc:mathstatKurssit.Bayesian_positive\.pdf]]
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112 (% style="color: rgb(0,102,102);" %)
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114 === (% style="color: rgb(0,102,102);" %)Examination(%%) ===
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116 * Monday, May 4.  16-19 in room B123. In addition to lecture material there will be one question either  from this [[attach:Article1.pdf]], or from this [[attach: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.
117 * Passing the course worth 6 cu is based on the examination and home-exercises. Examination gives you 5 cu and home-exercises 1 cu.
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119 === (% style="color: rgb(0,102,102);" %)Own project(%%) ===
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121 * [[doc:mathstatKurssit.Own project\.pdf]] is worth 2 cu.
122 * 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).
123 * In total you can get 9 cu from the course.