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@rdmpage @vizbi
TreeView
PHYLIP NJPLOT MacClade PAUP
Mature
Problem has been solved
Thank you
Any questions?
Trees suck…
…in ways that maps don’t
Maps are predictable
Navigation is predictable
Every pixel counts
Ground truth
Relative and absolute navigation
Latitude 42.363921Longitude -71.087763
Phylogeny has none of this
A B Y C D X
B A Y D C X We can reorder Y
@broadinstitute
B A Y D C X X is a partial order
B A Y D C X X is a partial order
B A Y D C X: evolutionary distance
B A Y D C X: time
Y Z? X What would third dimension represent?
Paloverde
@wellcometrust
Pretty, but…
Is 3D useful?
@systbiol
Y: evolutionary distance Z: genes/copies X: species
@DavKidd @andrewxhill Y: latitude Z: evolutionary distance X:longitude
@rdmpage
@andrewxhill
Touching the tree
@dr_pi
@kzelnio Think how great of a tool that could be at museums on a large flat screen at 4 year old height.
Dendroscope
Big trees
11 June 2003
“best viewed when enlarged to a 1.5-meter diameter”
add
@rdmpage
@rdmpage
1 2 3
1 4 2 5 3
What’s next… Geophylogenies Touch Zoomable viewers http://iphylo.blogspot.com

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Phylogeny VIZBI 2011

Editor's Notes

  1. http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
  2. http://evolution.genetics.washington.edu/phylip/software.html#Plotting and “A reference guide for tree analysis and visualization” http://dx.doi.org/10.1186/1756-0381-3-1
  3. http://loco.biosci.arizona.edu/paloverde/paloverde.html
  4. http://www.wellcometreeoflife.org/
  5. “Visualising very large phylogenetic trees in three dimensional hyperbolic space” http://dx.doi.org/10.1186/1471-2105-5-48
  6. June 2007 issue of Systematic Biology, a homage to Wayne Maddison, SystBiol (1997) 46 (3): 523-536. doi: 10.1093/sysbio/46.3.523
  7. Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization NamshinKim and ChristopherLeehttp://dx.doi.org/10.1186/1471-2105-8-213
  8. http://iphylo.blogspot.com/2007/06/earth-not-flat-official.html
  9. http://systbio.org/?q=node/184, see http://dx.doi.org/10.1080/10635150701266848
  10. Petra Isenberg, see “Interactive tree comparison for co-located collaborative information visualization” http://www.ncbi.nlm.nih.gov/pubmed/17968069 and http://innovis.cpsc.ucalgary.ca/Research/CollaborativeTreeComparison
  11. http://www.perceptivepixel.com/ and http://iphylo.blogspot.com/2008/08/perceptive-pixel-taxonomy-demo.html
  12. http://www.senchatouch.com/
  13. http://www-ab.informatik.uni-tuebingen.de/software/dendroscope
  14. Image from Mike Sanderson’s Lab (http://loco.biosci.arizona.edu/)
  15. http://msdn.microsoft.com/en-us/library/cc645050(v=vs.95).aspx
  16. http://iphylo.blogspot.com/2007/08/visualising-very-big-trees-part-iv.html