Slideshare uses cookies to improve functionality and performance, and to provide you with relevant advertising. If you continue browsing the site, you agree to the use of cookies on this website. See our User Agreement and Privacy Policy.

Slideshare uses cookies to improve functionality and performance, and to provide you with relevant advertising. If you continue browsing the site, you agree to the use of cookies on this website. See our Privacy Policy and User Agreement for details.

Like this presentation? Why not share!

- Taxonomy by Roderic Page 6790 views
- Phylogenetic analysis by National Institut... 5206 views
- Molecular Phylogenetic relationship... by Gayathri Amarakoon 116 views
- Aspergillus by siddhantamohanty 1172 views
- Polysaccharides structural diversit... by EducationCikale609 122 views
- exopolysaccharides by CHARLIE 346 views

No Downloads

Total views

3,675

On SlideShare

0

From Embeds

0

Number of Embeds

1,748

Shares

0

Downloads

40

Comments

3

Likes

2

No embeds

No notes for slide

- 1. Phylogeny
- 2. 2 Trees and their terms
- 3. 3
- 4. 4 Tree terminology edge (branch) leaf (terminal node) internal node (hypothetical ancestor) root
- 5. 5
- 6. 6 Rooting a tree
- 7. 7 Order doesn’t matter (trees are like mobiles) A B C D ABCD = AB C D =
- 8. 8 Tree description , )( , )( ( A( ,B )), C A CB
- 9. Building trees • Maximum parsimony (which tree can explain data with least amount of evolutionary change) • Maximum likelihood (which tree has highest probability of generating observed data) • Bayesian analysis (probability distribution of trees based on prior knowledge and current data)
- 10. 11 Types of substitution A G C T transitions transitions transversions
- 11. Likelihood 12 A C G T A C G T Observed A C G T A C G T Jukes-Cantor human chimp Predicted by models Kimura 2 parameter A C G T A C G T Hasegawa et al. A C G T A C G T •More parameters = better fit •but, don’t want too many parameters
- 12. Probability is different from likelihood
- 13. You hear a noise in the ceiling…
- 14. Could be elves bowling in the attic
- 15. The probability that you have bowling elves is very low…
- 16. …but if you did have them, the probability that you would hear them is very high (=likelihood)
- 17. Bayesian methods
- 18. • Probability of having bowling elves is low (prior probability) • If you have bowling elves, probability that they would make a noise is high (likelihood) • Bayesian methods combine prior probability with likelihood to get posterior probability
- 19. Bayesian posterior probabilities 1.0 0.8 0.5 A E B C D
- 20. Open problems
- 21. Visualisation
- 22. There are few constraints on how we can draw trees
- 23. X A B C D Y
- 24. X B A D C Y We can reorder Y
- 25. @broadinstitute
- 26. X B A D C Y X is a partial order
- 27. X B A D C Y X is a partial order
- 28. X: evolutionary distance B A D C Y
- 29. X: time B A D C Y
- 30. Y X Z? What would third dimension represent?
- 31. Paloverde
- 32. @wellcometrust
- 33. Touching the tree
- 34. @dr_pi
- 35. Big trees
- 36. add
- 37. @rdmpage
- 38. @rdmpage
- 39. Where are the trees?
- 40. http://www.treebase.org/
- 41. 47 0 1000 2000 3000 4000 5000 6000 7000 1975 1980 1985 1990 1995 2000 2005 Year Cumulative number Rate of growth of phylogenetic knowledge Number of papers with “molecular” and “phylogeny” in Web of Science Number of studies in TreeBASE
- 42. Why aren’t we archiving these trees?
- 43. How can we find the trees that we have?
- 44. TreeBASE interface
- 45. TreeBASE interface
- 46. Browser
- 47. The End

No public clipboards found for this slide

Why force the user to tell a computer what something is, get the computer to figure it out? Computers are good at that sort of thing. Just let people type stuff in and figure it out. And no one is going to put in 'dc:identifier=Tx1234', ever. If they put in Tx1234, or a DOI, or whatever, the computer is smart enough to figure that out. If it's a bare number, show the various possible interpretations. At no point should a user have to think.

In an ideal world, this would be a single text box and power users would be able to put 'dc:identifier=Tx1234' in there in the same way that you can put 'filetype:pdf' in a google search.