1. Extending the iPlant DE: A Phylogenetics Workflow

2. Infer the state of a continuous trait along a phylogeny and estimate its rate of evolution. Continuous Ancestral Trait Reconstruction

3. Ancestral state of Hawaiian lobelioids Lobelia niihauensis (Image: David Eickhoff) Cyanea leptostegia (Image: Karl Magnacca)

5. (Schulter et al. 1997, Paradis 2004) Continuous Ancestral Character Estimation Time

6. Obtain sequences GetSeq Obtain sequences GetSeq Align sequences Muscle Align sequences Muscle Build Tree Ninja (NJ) Build Tree Ninja (NJ) Integrate Data Lopper Integrate Data Lopper Run Analysis CACE DACE Contrast OUch Picante Penalized likelihood Run Analysis CACE DACE Contrast OUch Picante Penalized likelihood Traits Seq IDs

7. Obtain sequences GetSeq Obtain sequences GetSeq Align sequences Muscle Align sequences Muscle Build Tree Ninja (NJ) Build Tree Ninja (NJ) Integrate Data Lopper Integrate Data Lopper Run Analysis CACE Run Analysis CACE Traits Seq IDs CACE Phylogenetic Workflow

8. 1. Select the Apps 2. Order the Apps 3. Map Outputs to Inputs 4. Run the analysis As Easy as 1-2-3-4

9. Step 0 Become familiar with the Apps you are going to use: inputs, outputs and options. Modify as necessary.

10. HANDS ON / DEMO

17. Obtain sequences GetSeq Obtain sequences GetSeq Align sequences Muscle Align sequences Muscle Build Tree Ninja (NJ) Build Tree Ninja (NJ) Integrate Data Lopper Integrate Data Lopper Run Analysis CACE Run Analysis CACE Traits Seq IDs CACE Phylogenetic Workflow

18. Seq IDs

19. Traits

20. Seq IDs Traits