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Phylogeny inference and data analysis, spring 2013

Lecturer

Sirkka-Liisa Varvio

Scope

5-10 cu

Type

Intermediate/Advanced studies

Prerequisites

Basic probabilistics and interest in bio-applications of statistics.
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.

Period III, 4cr lecture/data-analysis module

First lecture Tue 22.1, 14-16 B120, 16-  C128

Period IV, 1-5cr project work module

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.

Content description

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.

Software and servers to be used during the course

MrBayes, BEAST v1.7.4., SplitsTree4, MEGA5, HyPhy, NCBI, MAFFT,

Grading

Assignments: 40 points, exam: 20 points = 60 points is the maximum.  Half of the maximum (30 points): grade 1 and 50 points: grade 5.

 


 Tue 22.1, 14-16 B120, 16- C128 (computer class)

For those not having background:
Background_lecture_220113.pdf,
Short tutorial article.pdf, Phylogenetics - Principles and practice.pdf
Instructions_for_background_exercise.pdf , Initial_dataset_for_the_exercise.txtUseful general background:
NCBI BLAST.pdf
, Multiple sequence alignment review.pdf, Collection of alignment tools.pdf


Tue 29.1, 16-  C128

This is for those who need tutoring with MEGA5. Read this: MEGA5.pdf  Background exercise with neighbor-joining and parsimony, bootstapping confidence.

Thu 31.1, 14-16 B120

Phylogeny_books_and_programs.pdf

Assignments explained:
Assignment 1 more comments added.pdf, mt_genomes.txt, mt_genomes_aligned.txt, cytB_cut_from_total genome.txt
Assignment 2 more comments added.pdfH1N1_pre_pandemic.txt,
H1N1_pre_pandemic_edit.fasta, human_pre_pandemic_2.fastahttp://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html
Assignment 3.pdf 
Assignment 4.pdf
Stat_2.pdf, Stat_3.pdf, , , Stat_6.pdf, Stat_7.pdf, Stat_8.pdf, Stat_9.pdf,
Appl_1.pdf, , Appl_4.pdf,, Appl_6.pdf,,,
Reserved topics:

 
MOODLE


Tue  5.2, 14-18 C128

Maximum_likelihood_and_Bayesian.pdf
Bayes-software demo. http://mrbayes.sourceforge.net/
Original MrBayes paper.pdf , MrBayes Manual.pdf,  The program version in C128 corresponds this manual: MrBayes Manual 3.1.pdfMrBayes Commands.pdf, MCMCMC.pdf, Traditional and Bayesian phylogeny estimation.pdf, This is useful clarification.pdf
Assignment 1 data by MrBayes.
For data conversion: http://sequenceconversion.bugaco.com/converter/biology/sequences/


Tue 12.2, 14-18  C128

Computer class working with assignments.


Tue 19.2, 14-18 C128  

Computer class working with assignments. Assignment submission dedlines have been extended to Mon 25.2.


See your email about info how to continue.  Home-exam and other issues.pdf

Network phylogenies.pdf
Collection of themes: Tree of life.pdf, Mammalian phylogeny.pdf, Human origins.pdf, Virus and bacteria epid tracing.pdf,  


 


MOODLE

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