Phylogeny inference and data analysis , spring 2012


Sirkka-Liisa Varvio

Scope, prerequisites

2-12 cu
Basic probabilistics and statistical inference are assumed as prerequisites.
The course is for intermediate/advanced statistics studies, suitable also for biology/bioinformatics students, and for Bioinformatics Master´s program (MBI).

2cu by an exam, based on lectures,
2cu by weekly assignments,
2cu by reading group (= reading, commenting, writing short reports on scientific papers),
4-6cr by a project in IV period. This will be working in computer class and at home, time schedule negotiable, topics to be agreed at the end of period III.

You can thus collect 2-12cr from the course, i.e. you can choose which modules you take.

Content scheme

The aim of the course is to familiarize both on statistical and biological aspects of phylogenies, i.e. trees and networks, which are elementary structures of differences among biological entities (species, individuals, genes, sequences in general), amenable to statistical inference. The major categories of phylogeny inference methods: distance matrix, parsimony, maximum likelihood, Bayesian, Network approaches.

Week 1

  • Introduction to reading group which operates via Moodle:
    The idea of the reading group is to introduce various applications of phylogeny inference, as well as statistical topics behind practical applications.
    This is the edited set of topics including reservations made so far:
    • READING GROUP TOPICS FOCUSING STATISTICS (duplicate reservations compensated by new topic suggestions)
      BICs and AICs in phylogenetics.pdf(Christian),
      Paradoxes and Bayesian phylogenetics.pdf (Alberto),
      Posterior prob how meaningful.pdf (Pedro),
      A prior for Bayesian phylo inference.pdf (Hailin),
      Distributions of bootstrap and posteriors.pdf (Teemu),
      Bootstrap vs posterior prob 1.pdf (Hilal),
      Bootstrapping confidence.pdf (Nico),
    • BIO-FOCUSED READING GROUP TOPICS (duplicate reservations should be compensated with suggested new topics)
      Human history tracing by Helicobacter.pdf (Suvi),
      Phylodynamics of microbes.pdf (Shinjini),
      HIV phylodynamics.pdf (Ilaria),
      Rates of evolutionary change in viruses.pdf (Roberta),
      Horizontal gene transfer in eukar evol.pdf (Chunxian),
      Pharmacophylogenomics.pdf, Drug discovery Phylogeny 2.pdf, Drug discovery Phylogeny 3.pdf, Drug discovery Phylogeny 4.pdf, (Nicole, Ayesha: look at three new papers and think about choosing instead of the first paper one of these),
      Language phylogenies.pdf (Jimmy),
      Protein evolution.pdf (Jian),
      Cancer phylo algorithmics.pdf (Poojitha),
      Evolutionary scenario for flower origins.pdf (Roman),
      Microbiome phylotyping.pdf (Shafiqul),

Mammalian karyotype evolution.pdf, Cancer phylogenomics.pdf, Listeria virulence phylo.pdf, Papillomavirus phylo tracing.pdf, HGT Eukaryote evol 2.pdf, HGT Eukaryote evol 3.pdf,

Week 2

  • Tue 24. Jan, 14-16, C128
    This lecture/computer session is for those that lack previous experience on working with biological sequences.
    For those that have taken the course Genetic analysis and molecular evolution (or something like that), assignment 1 has enough background without participating the lecture.
  • Thu 26. Jan, 14-16, B120,

Week 3

  • Thu 2. Feb, 14-16, B120 and in computer class C128.
    • Maximum likelihood.pdf
    • Bayesian phylogeny inference - Lecture 1.pdf
    • Original MrBayes paper.pdf, MCMCMC.pdf, Traditional and Bayesian phylogeny estimation.pdf
    •, This new Manual version lacks some chapters: MrBayes Manual.pdf, Use this Manual: MrBayes Manual 3.1.pdf, Useful background.pdf, MrBayes Commands.pdf.
    • During the computer class session example dataset from MrBayes folder.
    • Assignment 2.pdf

Week 4

Week 5

Week 6

  • Thu 23. Feb, 16 -> in computer class C128
    • Assignment presentations. See Moodle-page for further information.

Week 7


Part II

Pedro, Ilaria and Roberta: mtgenset.txt, mtgenset_mega.txt, mtgenset.nxs
^cat.txt (this file is under corrections), cat.pdf
Ilaria and Roberta:
killer_whale.txt (This is the original non-aligned file. Use the following aligned files which are ready for MEGA and Splitstree, and also for MrBayes if you want to use that program, too: killer_whale.FASTA, killer_whale.nxs whale.pdf
horse.txt (this file is under corrections), horse.pdf, horse_suppl.pdf


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