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Post-tree Analyses Workflow


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Phylogenetic Workflows Part II: Post-tree Analyses
Given at the Botany 2011 Conference

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Post-tree Analyses Workflow

  1. 1. Phylogenetic Workflows Part II Post-tree Analyses Naim Matasci The iPlant Collaborative Botany 2011 July 8-14, 2011
  2. 2. <ul><li>Obtain sequences </li></ul><ul><li>GetSeq </li></ul><ul><li>Align sequences </li></ul><ul><li>Muscle </li></ul><ul><li>Build Tree </li></ul><ul><li>FastTree (aML) </li></ul><ul><li>Ninja (NJ) </li></ul><ul><li>PHYLIP (MP, NJ, ML) </li></ul><ul><li>Visualize Tree </li></ul><ul><li>iPlant Tree Viewer </li></ul><ul><li>Integrate Data </li></ul><ul><li>Lopper </li></ul><ul><li>TNRS </li></ul><ul><li>Run Analysis </li></ul><ul><li>CACE </li></ul><ul><li>DACE </li></ul><ul><li>Contrast </li></ul><ul><li>OUch </li></ul><ul><li>Picante </li></ul><ul><li>Penalized likelihood </li></ul>
  3. 3. Merge Datasets <ul><li>Combine trees, character matrices and taxa list to create new datasets </li></ul>
  4. 6. Visualize phylogenies <ul><li>Visualize your data </li></ul>
  5. 7. Phylozoom <ul><li>Explore the Tree of Life, from the root to the leaves </li></ul>
  6. 8. Phylogenetically independent contrasts <ul><li>Remove the effect of shared ancestry for observed character correlations </li></ul>
  7. 9. Do traits evolve in concert? Modified from Ackerly et al.
  8. 10. Contrasts
  9. 11. Discrete ancestral trait reconstruction <ul><li>Infer the state of a discrete trait along a phylogeny and estimate its rate of evolution </li></ul>
  10. 12. Ancestral state of Hawaiian lobelioids Lobelia niihauensis : David Eickhoff, Cyanea leptostegia : Karl Magnacca Lobelia niihauensis (Image: David Eickhoff) Cyanea leptostegia (Image: Karl Magnacca)