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2 >>url:https://moodle.helsinki.fi/course/view.php?id=8779||shape="rect"]]
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4 = (% style="color: rgb(0,51,102);" %)Phylogeny inference and data analysis, spring 2013(%%) =
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6 === (% style="color: rgb(0,51,102);" %)Lecturer(%%) ===
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8 [[Sirkka-Liisa Varvio>>doc:mathstatHenkilokunta.Varvio, Sirkka-Liisa]]
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10 === (% style="color: rgb(0,51,102);" %)Scope(%%) ===
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12 5-10 cu
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14 === (% style="color: rgb(0,51,102);" %)Type(%%) ===
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16 Intermediate/Advanced studies
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18 === (% style="color: rgb(0,51,102);" %)Prerequisites(%%) ===
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20 Basic probabilistics and interest in bio-applications of statistics.
21 The course is suitable for students with planned orientation to biometry and bioinformatics and also for other students interested in biological applications of statistical inference.
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23 ===== (% style="color: rgb(0,51,102);" %)Period III, 4cr lecture/data-analysis module(%%) =====
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25 First lecture Tue 22.1, 14-16 B120, 16-  C128(% style="color: rgb(0,51,102);" %)
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28 ===== (% style="color: rgb(0,51,102);" %)Period IV, 1-5cr project work module(%%) =====
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30 Optional (for extending the 5cr to 10cr) project topics will be discussed at the end of III period. Working is according to student´s own time schedule.
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32 === (% style="color: rgb(0,51,102);" %)Content description(%%) ===
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34 Past practice on phylogenetics was to describe relationships among species within the disciplines systematics and taxonomy. Today the scope is much wider. Phylogenetics is used as a necessary tool in all kind of bioscience research questions: relationships among genes, gene families, alleles, cell lines, various genomic components, histories of populations, evolutionary and epidemiological dynamics of bacteria and viruses, etc.. Phylomics is the natural extension of genomics and metagenomics, phylotyping the current way of understanding ecosystems within and outside organisms (environments). During the course we familiarize with applications, statistical frameworks, analyse data during computer class sessions by using several software-packages.
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36 ===== (% style="color: rgb(0,51,102);" %)Software and servers to be used during the course
37 (%%) =====
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39 (% class="confluence-link" style="color: rgb(0,51,102);" %)[[MrBayes,>>url:http://mrbayes.sourceforge.net/||shape="rect"]] [[BEAST v1.7.4.>>url:http://beast.bio.ed.ac.uk/Main_Page||shape="rect"]], [[SplitsTree4>>url:http://www.splitstree.org/||shape="rect"]][[, >>url:http://www.splitstree.org/||shape="rect"]][[MEGA5>>url:http://www.megasoftware.net/||shape="rect"]][[, >>url:http://www.splitstree.org/||shape="rect"]][[HyPhy>>url:http://hyphy.org/w/index.php/Main_Page||shape="rect"]][[, >>url:http://www.splitstree.org/||shape="rect"]][[NCBI>>url:http://www.ncbi.nlm.nih.gov/||shape="rect"]][[, >>url:http://www.splitstree.org/||shape="rect"]][[MAFFT,>>url:http://mafft.cbrc.jp/alignment/server/||shape="rect"]]
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42 ===== (% style="color: rgb(0,51,102);" %)Grading(%%) =====
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44 (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)Assignments: 40 points, exam: 20 points = 60 points is the maximum.  Half of the maximum (30 points): grade 1 and 50 points: grade 5(% style="color: rgb(0,51,102);" %).
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46 (% style="color: rgb(0,51,102);" %)
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50 (% style="color: rgb(0,51,102);" %) **Tue 22.1, 14-16 B120, 16- C128 (computer class)**
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52 (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(255, 0, 0); color: rgb(0, 0, 0)" %)For those not having background: (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)
53 (% class="confluence-link" %)Background_lecture_220113.pdf(%%),
54 (% class="confluence-link" %)Short tutorial article.pdf(%%), (% class="confluence-link" %)Phylogenetics - Principles and practice.pdf(%%)
55 (% class="confluence-link" %)Instructions_for_background_exercise.pdf(%%) , (% class="confluence-link" %)Initial_dataset_for_the_exercise.txtUseful general background:
56 (% class="confluence-link confluence-link" %)NCBI BLAST.pdf(%%), (% class="confluence-link" %)Multiple sequence alignment review.pdf(%%), (% class="confluence-link" %)Collection of alignment tools.pdf(%%)
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61 (% style="color: rgb(0,51,102);" %)**Tue 29.1, 16-  C128**
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63 This is for those who need tutoring with MEGA5. Read this: (% class="confluence-link" %)MEGA5.pdf(%%)  Background exercise with neighbor-joining and parsimony, bootstapping confidence.
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65 (% style="color: rgb(0,51,102);" %)**Thu 31.1, 14-16 B120**
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67 (% style="color: rgb(255, 0, 0); color: rgb(0, 0, 0)" class="confluence-link" %)Phylogeny_books_and_programs.pdf
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69 (% style="color: rgb(255, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 51, 102)" %)**Assignments explained**(% style="color: rgb(255, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %):(% style="color: rgb(255, 0, 0); color: rgb(0, 0, 0)" %)
70 (% class="confluence-link" %)Assignment 1 more comments added.pdf(%%), (% class="confluence-link" %)mt_genomes.txt(%%), (% class="confluence-link" %)mt_genomes_aligned.txt(%%), (% class="confluence-link" %)cytB_cut_from_total genome.txt(%%)
71 (% class="confluence-link" %)Assignment 2 more comments added.pdf(%%),  (% class="confluence-link" %)H1N1_pre_pandemic.txt(%%),(%%) (% class="confluence-link" %)H1N1_pre_pandemic_edit.fasta(%%), (% class="confluence-link" %)human_pre_pandemic_2.fasta(%%),  [[http:~~/~~/www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html>>url:http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html||shape="rect"]]
72 (% class="confluence-link" %)Assignment 3.pdf(%%) 
73 (% class="confluence-link" %)Assignment 4.pdf(%%)
74 (% class="confluence-link" %)Stat_2.pdf(%%), [[attach:Stat_3.pdf]], , , (% class="confluence-link" %)Stat_6.pdf(%%), (% class="confluence-link" %)Stat_7.pdf(%%), (% class="confluence-link" %)Stat_8.pdf(%%), (% class="confluence-link" %)Stat_9.pdf(%%),
75 (% class="confluence-link" %)Appl_1.pdf(%%), , (% class="confluence-link" %)Appl_4.pdf(%%)~,~, (% class="confluence-link" %)Appl_6.pdf(%%)~,~,,(% class="confluence-link" %)
76 (%%)Reserved topics:
77 \\(% style="color: rgb(255,0,0);" %)
78 (%%)**[[MOODLE>>url:https://moodle.helsinki.fi/course/view.php?id=8779||shape="rect"]]**
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82 (% style="color: rgb(0,51,102);" %)**Tue  5.2, 14-18 C128**
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84 (% class="confluence-link" %)Maximum_likelihood_and_Bayesian.pdf(%%)
85 Bayes-software demo. [[http:~~/~~/mrbayes.sourceforge.net/>>url:http://mrbayes.sourceforge.net/||shape="rect"]]
86 (% class="confluence-link" %)Original MrBayes paper.pdf(%%) , (% class="confluence-link" %)MrBayes Manual.pdf(%%),  The program version in C128 corresponds this manual: (% class="confluence-link" %)MrBayes Manual 3.1.pdf(%%),  (% class="confluence-link" %)MrBayes Commands.pdf(%%), (% class="confluence-link" %)MCMCMC.pdf(%%), (% class="confluence-link" %)Traditional and Bayesian phylogeny estimation.pdf(%%), (% class="confluence-link" %)This is useful clarification.pdf(%%)
87 Assignment 1 data by MrBayes.
88 For data conversion: [[http:~~/~~/sequenceconversion.bugaco.com/converter/biology/sequences/>>url:http://sequenceconversion.bugaco.com/converter/biology/sequences/||shape="rect"]]
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92 (% style="color: rgb(0,51,102);" %)**Tue 12.2, 14-18  C128**
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94 Computer class working with assignments.
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98 (% style="color: rgb(0,51,102);" %)**Tue 19.2, 14-18 C128 **(% style="color: rgb(0, 51, 102); color: rgb(255, 0, 0)" %) (% style="color: rgb(0,51,102);" %)**
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101 Computer class working with assignments. (% style="color: rgb(255,0,0);" %)Assignment submission dedlines have been extended to Mon 25.2.
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105 (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(255, 0, 0)" %)**See your email about info how to continue.**(% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)  (% class="confluence-link" %)Home-exam and other issues.pdf(%%)
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108 (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" class="confluence-link" %)Network phylogenies.pdf(% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)
109 Collection of themes: Tree of life.pdf, Mammalian phylogeny.pdf, Human origins.pdf,(% style="color: rgb(0,51,102);" %) (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)Virus and bacteria(% style="color: rgb(0,51,102);" %) (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)epid tracing(% style="color: rgb(0,51,102);" %).(% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)pdf(% style="color: rgb(0,51,102);" %), (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %) (% style="color: rgb(0,51,102);" %)
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118 ===== [[MOODLE>>url:https://moodle.helsinki.fi/course/view.php?id=8779||shape="rect"]] =====
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120 === [[Registration>>url:https://oodi-www.it.helsinki.fi/hy/opintjakstied.jsp?html=1&Tunniste=57729||shape="rect"]] ===
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122 Did you forget to register? [[What to do>>doc:mathstatOpiskelu.Kysymys4]].