Phylogeny VIZBI 2011

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Slides from talk for VizBi 2011 http://vizbi.org/

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  • http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
  • 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
  • http://loco.biosci.arizona.edu/paloverde/paloverde.html
  • http://www.wellcometreeoflife.org/
  • “Visualising very large phylogenetic trees in three dimensional hyperbolic space” http://dx.doi.org/10.1186/1471-2105-5-48
  • June 2007 issue of Systematic Biology, a homage to Wayne Maddison, SystBiol (1997) 46 (3): 523-536. doi: 10.1093/sysbio/46.3.523
  • 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
  • http://iphylo.blogspot.com/2007/06/earth-not-flat-official.html
  • http://systbio.org/?q=node/184, see http://dx.doi.org/10.1080/10635150701266848
  • 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
  • http://www.perceptivepixel.com/ and http://iphylo.blogspot.com/2008/08/perceptive-pixel-taxonomy-demo.html
  • http://www.senchatouch.com/
  • http://www-ab.informatik.uni-tuebingen.de/software/dendroscope
  • Image from Mike Sanderson’s Lab (http://loco.biosci.arizona.edu/)
  • http://msdn.microsoft.com/en-us/library/cc645050(v=vs.95).aspx
  • http://iphylo.blogspot.com/2007/08/visualising-very-big-trees-part-iv.html
  • Phylogeny VIZBI 2011

    1. 1. @rdmpage<br />@vizbi<br />
    2. 2. TreeView<br />
    3. 3. PHYLIP<br />NJPLOT<br />MacClade<br />PAUP<br />
    4. 4.
    5. 5.
    6. 6. Mature<br />
    7. 7. Problem has been solved<br />
    8. 8. Thank you<br />
    9. 9. Any questions?<br />
    10. 10. Trees suck…<br />
    11. 11. …in ways that maps don’t<br />
    12. 12. Maps are predictable<br />
    13. 13.
    14. 14.
    15. 15. Navigation is predictable<br />
    16. 16.
    17. 17. Every pixel counts<br />
    18. 18.
    19. 19.
    20. 20. Ground truth<br />
    21. 21.
    22. 22.
    23. 23.
    24. 24.
    25. 25. Relative and absolute navigation<br />
    26. 26.
    27. 27. Latitude 42.363921Longitude -71.087763<br />
    28. 28. Phylogeny has none of this<br />
    29. 29. A<br />B<br />Y<br />C<br />D<br />X<br />
    30. 30. B<br />A<br />Y<br />D<br />C<br />X<br />We can reorder Y<br />
    31. 31. @broadinstitute<br />
    32. 32. B<br />A<br />Y<br />D<br />C<br />X<br />X is a partial order<br />
    33. 33. B<br />A<br />Y<br />D<br />C<br />X<br />X is a partial order<br />
    34. 34. B<br />A<br />Y<br />D<br />C<br />X: evolutionary distance <br />
    35. 35. B<br />A<br />Y<br />D<br />C<br />X: time<br />
    36. 36. Y<br />Z?<br />X<br />What would third dimension represent?<br />
    37. 37. Paloverde<br />
    38. 38. @wellcometrust<br />
    39. 39.
    40. 40. Pretty, but…<br />
    41. 41. Is 3D useful?<br />
    42. 42. @systbiol<br />
    43. 43. Y: evolutionary distance<br />Z: genes/copies<br />X: species<br />
    44. 44.
    45. 45. @DavKidd<br />@andrewxhill<br />Y: latitude<br />Z: evolutionary distance<br />X:longitude<br />
    46. 46. @rdmpage<br />
    47. 47. @andrewxhill<br />
    48. 48. Touching the tree<br />
    49. 49. @dr_pi<br />
    50. 50. @kzelnio<br />Think how great of a tool that could be at museums<br />on a large flat screen at 4 year old height.<br />
    51. 51.
    52. 52.
    53. 53. Dendroscope<br />
    54. 54.
    55. 55. Big trees<br />
    56. 56. 11 June 2003<br />
    57. 57. “best viewed when enlarged to a 1.5-meter diameter”<br />
    58. 58. add<br />
    59. 59.
    60. 60.
    61. 61. @rdmpage<br />
    62. 62. @rdmpage<br />
    63. 63. 1<br />2<br />3<br />
    64. 64. 1<br />4<br />2<br />5<br />3<br />
    65. 65. What’s next…<br />Geophylogenies<br />Touch<br />Zoomable viewers<br />http://iphylo.blogspot.com<br />

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