Dr. O. Reva: Phylogenetic Workshop for Beginners
Bioinformatics and Computational Biology Unit,
Department of Biochemistry, University of Pretoria
Tel: 012-420-5810
Fax: 012-420-5800
E-Mail: oleg.reva@up.ac.za
1. Catalogue category and sub-category:
Natural science, phylogenetics.
2. Description
Phylogenetic trees are the most popular graphs widely used in scientific publications to demonstrate
relationships between organisms. Many software tools are available on-line which build
phylogenetic trees from the data provided by users, however, many of them do not explain neither
requirements for the datasets nor the limitations associated with the method of choice. This
workshop is to teach biological students and staff members how to prepare the initial data for a
phylogenetic study and how to choose the most appropriate algorithm of tree calculation.
3. Target audience
Students and staff members interested in phylogenetic approaches to investigate ancestral
relationships between genes, proteins and organisms and to reconstruct evolutionary processes and
changes on different levels from nucleotide sequences to complete genomes.
4. Outline of Course Content
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Sequence generation
o Sanger capillary sequencing and the next generation sequencing – new
opportunities and challenges;
o Quality control of base calling;
o Sequence assembly and alignment;
o Looking for sequences in public databases;
Basics, terminology and parameters of phylogenetic analysis
o Data formats, sequence alignment and alignment edition;
o Rooted and unrooted trees, outgroup definition;
o Cladograms, additive and ultrametric trees;
o Similarity versus homology, homology versus orthology and paralogy;
o Homoplasy: finding and removal of homoplastic characters;
Sequence alignment, tree building and sequence assembly software
o PHYLIP 3.69 (http://evolution.gs.washington.edu/phylip/getme.html)
o JALVIEW (http://www.jalview.org/)
o MEGA5 beta (http://www.megasoftware.net/beta/mega.php)
o TREE-PUZZLE (http://www.tree-puzzle.de/)
o Phylemon’s on-line tools (http://phylemon.bioinfo.cipf.es/cgi-bin/tools.cgi)
o BioEdit (http://www.mbio.ncsu.edu/BioEdit/page2.html)
o Staden Package (http://staden.sourceforge.net/)
Primers of phylogenetic analysis
o Distance matrix based, parsimony and maximal likelihood phylogenetic trees;
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Selection of the most appropriate algorithm and model for a phylogenetic analysis of
a given dataset;
o Phylogenetic analysis based on allele frequencies and continuous data;
o Statistical assessment of phylogenetic trees, consensus trees;
Additional topics to consider
o Pipelining of phylogenetic studies by using MS-DOS batch files;
o Basics of phylogenomics – comparison of complete genome sequences by
oligonucleotide usage patterns.
5. Learning Outcome
After completion of the training, learners will:
 Understand the basics and principals of selection and preparation of biological materials for
phylogenetic studies;
 Be prepared for a knowledge based choice of the best algorithm and evolutionary model to
resolve a given practical task;
 Be able to perform a statistical assessment of resulted phylogenetic trees;
 Be able to prepare an informative and professionally looking tree graphs for scientific
publications.
6. Who should attend
This workshop will be aiding for any learners from undergraduate students to senior lecturer and
researchers who is interested in using phylogenetic trees in their work or study.
7. Entry requirement
Basic knowledge of DNA and genetics
8. Other entry requirement
Candidates should have some experience with computer based approaches of manipulation of DNA
and protein sequence data at least at the level of sequence alignment.
9. Contact days: 5
10. Hours per day: 8
11. Course composition: single module
12. Assessment type: assignment test
13. Medium of instruction: English
14. Suggested course fee: not applicable
15. Related courses: sequencing, bioinformatics
16. Facilitator
Dr Oleg Reva
Tel. +27(0)-12-420-5810
E-Mail: oleg.reva@up.ac.za