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- Introduction to reading group which operates via Moodle: https://moodle.helsinki.fi/course/view.php?id=5840
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),
- READING GROUP TOPICS FOCUSING STATISTICS (duplicate reservations compensated by new topic suggestions)
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,
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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.
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- 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
- http://mrbayes.sourceforge.net/, 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
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Week 4
- Thu 9. Feb, 14-16, B120 and 16 -> in computer class C128
- Assignment 3.pdf, Data:H1N1_fasta.txt, H1N1.nex, bact_fasta.txt,
link to converter: http://sequenceconversion.bugaco.com/converter/biology/sequences/
- Assignment 3.pdf, Data:H1N1_fasta.txt, H1N1.nex, bact_fasta.txt,
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- Thu 16. Feb, 14-16, B120 and 16 -> in computer class C128
- Network phylogenies.pdf, Median-joining networks.pdf, Network phylogeny examples.pdf
- Assignment 4.pdf, Link to mtDNA database: http://www.mtdb.igp.uu.se/
- http://www.splitstree.org/, http://www.fluxus-engineering.com/sharenet.htm
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Projects
Pedro, Ilaria and Roberta: mtgenset.txt, mtgenset_mega.txt, mtgenset.nxs
Pedro:
^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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Registration
Did you forget to register? What to do.