1. Build an Automated Workflow Visual Workflow Creator Discovery Environment

2. iPlant Discovery Environment Demo workflow – align sequences and build ML tree Add Apps to workflow Launch workflow Monitor the job progress and view results Task: Create a workflow that will build a multiple alignment of sequences from a FASTA file and then compute a maximum likelihood phylogenetic tree.

3. iPlant Discovery Environment Demo workflow – align sequences and build ML tree Tip: Not every App can be integrated into a workflow, some limitations: Currently only linear workflows may be created. Apps to be used must have inputs and outputs that have been described in metadata by the App’s integrator. In some cases you may edit the App to make it compatible. If an App prepends part of the input filename onto the output filename, currently the App cannot be included in a workflow

4. Log in to Discovery Environment

5. iPlant Discovery Environment Add Apps to workflow Demo workflow – align sequences and build ML tree

6. 1.Click on Apps 2.Click Create and select Workflow iPlant Discovery Environment Demo workflow – align sequences and build ML tree

7. 3.On the Automate Workflow window click Switch View 4.Edit the workflow name and description 5.Search for MUSCLE 3.8.31 and drag the App into the workflow builder 6.Search for RAxML-7.3.0 and drag the app into the workflow builder iPlant Discovery Environment Demo workflow – align sequences and build ML tree

8. 7.Expand the outputs of Muscle-3.8.31 App 8.Drag the phylip_interleaved.aln output into the input option of RAxML-7.3.0 9.Click Save iPlant Discovery Environment Demo workflow – align sequences and build ML tree

9. iPlant Discovery Environment Launch workflow Demo workflow – align sequences and build ML tree

10. iPlant Discovery Environment Demo workflow – align sequences and build ML tree 10.Click on Apps 11.Launch your workflow (Apps ‘Workspace’ section)

11. If desired: Enter a name/description for the analysis Choose an alternative output folder for the analysis iPlant Discovery Environment Demo workflow – align sequences and build ML tree

12. iPlant Discovery Environment Demo workflow – align sequences and build ML tree 12.Click on Muscle-3.8.31 -Select input data 13.For ‘Select Multiple Sequence File (FASTA format)’ Click Browse and locate the input file: Community Data > iplant_training > intro_phylogenetics > 01_input_data >atpB.fa

13. iPlant Discovery Environment Demo workflow – align sequences and build ML tree 14.Click on RAxML-7.3.0 –Sequence type 15.Select DNA 16.Click on RAxML-7.3.0 Select input data 17.For ‘Sequence Type’ select DNA; click Launch Analysis

14. iPlant Discovery Environment Monitor the job progress and view results Demo workflow – align sequences and build ML tree

15. 18.Click on Analyses 19.Monitor job until status is ‘Completed’ 20.Click on the job name to view the result of the job iPlant Discovery Environment Demo workflow – align sequences and build ML tree

16. iPlant Discovery Environment Demo workflow – align sequences and build ML tree Sample output from MUSCLE – RAxML workflow

17. Need more help? ask.iplantcollaborative.org

18. The iPlant Collaborative is funded by a grant from the National Science Foundation Plant Cyberinfrastructure Program (#DBI-0735191).