1. Applied Bioinformatics Week 8 Jens Allmer

2. Theory I

3. Phylogeny Sources –Sequences –Clades –Organisms Why –Understand evolution –Strain diversity –Epidemiology –Gene predicion

4. ? globin plants Ath-g analogs

5. Dendrogram http://en.wikipedia.org/wiki/Dendrogram

6. Phylogenetic Tree

7. Tree Terminology All circled elements (e.g.: a) are called node(s) The connections between them are called edge(s) or branch(es) The first node that forms the tree is called root (here abcdef) Terminal nodes that have only one connection are called leaf(ves) (e.g.: a) Unrooted Trees (remove red root)

8. Branch Length Arbitrary Similarity Evolutionary Time

9. Tree types A dendrogram is a broad term for the diagrammatic representation of a phylogenetic tree. A cladogram is a tree formed using cladistic methods. This type of tree only represents a branching pattern, i.e., its branch lengths do not represent time. A phylogram is a phylogenetic tree that explicitly represents number of character changes through its branch lengths. A chronogram is a phylogenetic tree that explicitly represents evolutionary time through its branch lengths.

10. Sequences DNA –Sensitive but quite divergent at longer distances –Use for very closely related organisms cDNA –Still sensitve but less divergent (e.g. introns) –Use for closely related families Protein –Least sensitive but most useful for more distant relationships –Use for distantly related species 16S RNA –Exists in all organisms –Highly conserved

11. Overall Process Get Sequences Construct MSA Compute pairwise distances (for some methods) Build Tree –Topology –Branch Lengths Estimate accuracy, reliability –Build several different trees for that Visualize the tree

12. Computational Tree Formation Distance Methods –Neighbor-Joining –Least-Squares –UPGMA Parsimony –Least number of evolutionary steps Maximum Likelihood –Highest probable tree to fit to the hypothesis is constructed

13. Neighbor Joining Bottom-up clustering method 1.Create distance map 2.Join closest nodes 3.Do (1-2) until fully joined http://en.wikipedia.org/wiki/Neighbor_joining

14. Least Squares Standard approximation approach –Minimizes the sum of the error (squares) Example PGLS –Phylogenetic Generalized Least Squares –Needs additional data (traits) http://www.dynamicgeometry.com/General_Resources/Advanced_Sketch_Gallery/Other_Explorations/Statistics_Collection/Least_Squares.html

15. UPGMA Unweighted Pair Group Method with Arithmetic Mean –Aglomerative hierarchial clustering method –Assumes constant rate of evolution

16. Similarity Measures Sequence –Number of different positions –Weighted differences Substitution Matrices –Pairwise alignments NW, SW,.. Additional measurements or knowlege –Traits Parsimony –Number of changes for tree paths

17. Tree Accuracy Bootstrapping –Resample –Recompute –Do many times –Compare results http://www.sciencedirect.com/science/article/pii/S0191814107000156

18. http://goergen.deviantart.com/art/Magic-Forrest-Wallpaper-139108299

19. End Theory I Mindmap Break

20. Practice I

21. Where to get Trees Most servers that allow for MSA will also provide at least the guide tree which was used to construct the alignment If that’s all you are interested in you don’t need to go any further

22. Edit your MSA Remove blocks consisting of mostly gaps (using JalView) Remove N- and C-termini if not conserved well

23. Easy Tree www.ebi.ac.uk/clustalw/ Paste your alignment Select a tree type Other options need to be set (see right) Press run Make a screen shot You can paste it where needed

24. Phylip (More elaborate tree) http://bioweb.pasteur.fr/seqanal/phylogeny/ phylip-uk.html Choose protdist from the page Paste the MSA Bootstrapping e.g.:

25. Phylip Run the query Click further analysis

26. Click Run Select full screen view There is your tree

27. Ugly Tree Let’s face it the tree is quite ugly http:// iubio.bio.indiana.edu/treeapp/treeprint-form.html Select the consense.outtree from the previous website and paste it into the box Select submit to create the tree Play around with the formats and settings

28. Tree Topologies

31. Other Resources http://en.wikipedia.org/wiki/List_of_phylog enetics_software http://itol.embl.de/

32. MSA http://www.ebi.ac.uk/clustalw http://www.tcoffee.org http://www.drive5.com/muscle Try all the above and compare the resulting MSAs

33. Editing Alignments http://www.jalview.org Start the applet Choose File – Input Alignment – from Textbox Copy and paste the ClustalW alignment

34. Playtime Be creative Explore the functions For saving you need to install locally JAVA applets are not allowed to save to your computer