This document discusses challenges and opportunities in visualizing phylogenetic trees. It notes that while maps have predictable navigation, trees can be drawn in many different ways. The document explores using additional dimensions like time, latitude and longitude to represent evolutionary relationships. It highlights projects like GenGIS, OneZoom and Dendroscope that attempt to make large trees more intuitive to navigate. Finally, it questions why more phylogenetic trees are not archived in databases and how software could generate publication-quality visualizations directly from analyses.

1. Visualising phylogenies
(a personal view)
@rdmpage
http://iphylo.blogspot.com

2. Trees suck…
http://vimeo.com/26210611

3. …in ways that maps don’t

4. Maps are predictable

7. Navigation is predictable

9. Every pixel counts

12. Ground truth

17. Relative and absolute navigation

18. Latitude 42.363921
Longitude -71.087763

19. Phylogeny has none of this

20. There are few constraints on how
we can draw trees

21. X
A
B
C
D
Y

22. X
B
A
D
C
Y
We can reorder Y

23. @broadinstitute

24. X
B
A
D
C
Y
X is a partial order

25. X
B
A
D
C
Y
X is a partial order

26. X: evolutionary distance
B
A
D
C
Y

27. X: time
B
A
D
C
Y

28. Y
X
Z?
What would third dimension represent?

29. @wellcometrust

30. Pretty, but…

31. Is 3D useful?

32. @systbiol

33. Y:latitude
X:longitude
Z: evolutionary distance
@DavKidd @andrewxhill

34. @rdmpage

35. GenGIS
2D geographically
ordered tree
@rob_beiko

36. GenGIS-style trees on
Google Maps
@rdmpage

37. Challenges
• Does 3D have a role beyond being a gimmick?
• Geospatial phylogenies

38. Big trees

39. 11 June 2003

40. “best viewed when enlarged to a 1.5-meter diameter”

41. add

44. @rdmpage

45. @rdmpage

46. OneZoom

47. http://tree.opentree.org

48. Challenges
• A visualisation of large trees that is as intuitive
and as useful as Google Maps
• A platform, not a picture

49. Touching the tree

50. @dr_pi

51. @kzelnio Think how great of a tool that could be at museums
on a large flat screen at 4 year old height.

53. Dendroscope

54. Build-a-Tree
https://lifeonearth.seas.harvard.edu/learning-activities/bat/

55. Challenges
• Intuitive, easy to use touchable trees
• Teaching and research
• Gamefication

56. Where are the trees?

57. http://www.treebase.org/

58. 58
0
1000
2000
3000
4000
5000
6000
7000
1975 1980 1985 1990 1995 2000 2005
Year
Cumulativenumber
Rate of growth of phylogenetic knowledge
Number of papers with
“molecular” and
“phylogeny” in Web of
Science
Number of
studies in
TreeBASE

59. Why aren’t we archiving these trees?
http://dx.doi.org/10.1371/journal.pbio.1001636 (2013)

62. Challenges
• Interactive trees for publications and
databases (eventually database = publication)
• Software to create pretty, machine readable
visualisations

63. Tree challenges
Big trees Touch Accessibility