Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.
Gene Tree/Species TreeReconciliationPhylotastic Hackathon    June 4, 2012
iPlant Tree of Life (iPTOL)• Tree Reconciliation• Big Trees• Data Assembly• Trait Evolution• Data Integration• Tree Visual...
Gene Tree ReconciliationProjection of gene trees onto a species tree•   gene duplications•   gene losses•   lineage sortin...
Gene Tree Reconciliation• Locating gene duplications allows us to  identify orthologs and paralogs• Identify gene composit...
Existing TR Cyberinfrastructure  Generate         EC       VisualizeReconciliations   Gene    Reconciliations             ...
Extending TR Cyberinfrastructure• Increased interoperability among the  component pieces• Query the location of gene dupli...
Extending TR Cyberinfrastructure  Generate                       VisualizeReconciliations     Gene       Reconciliations  ...
Tree Reconciliation GUI
Tree Reconciliation GUI
Tree Reconciliation GUI
Tree Reconciliation GUI                 Queries                 • BLAST                 • GO Term                 • Locus ...
Current Limitations• Users query against a pre-computed set of  reconciliations  • We generate the species trees  • We gen...
Making TR Phylotastic• Allow users to generate reconciliations  using their own data  • Supply a species tree OR  • Supply...
Phylotastic Components• Name resolution  • Given a gene tree or alignments determine the    species list• Tree Pruner    •...
A Phylotastic DNA Subway ..
Upcoming SlideShare
Loading in …5
×

Phylotastic reconciliation

605 views

Published on

Author: Jamie Estill

Published in: Technology, Business
  • Be the first to comment

  • Be the first to like this

Phylotastic reconciliation

  1. 1. Gene Tree/Species TreeReconciliationPhylotastic Hackathon June 4, 2012
  2. 2. iPlant Tree of Life (iPTOL)• Tree Reconciliation• Big Trees• Data Assembly• Trait Evolution• Data Integration• Tree Visualization
  3. 3. Gene Tree ReconciliationProjection of gene trees onto a species tree• gene duplications• gene losses• lineage sorting• horizontal transfer
  4. 4. Gene Tree Reconciliation• Locating gene duplications allows us to identify orthologs and paralogs• Identify gene composition in inferred ancestral genomes• Map of the positions of ancestral polyploidy events• Contribute to the study of the “fate” of duplicated genes• Address questions of gene family coevolution
  5. 5. Existing TR Cyberinfrastructure Generate EC VisualizeReconciliations Gene Reconciliations Trees TreeBeST primeTV primeGSR fltreebest
  6. 6. Extending TR Cyberinfrastructure• Increased interoperability among the component pieces• Query the location of gene duplications on the species tree• Integrate tree visualization tools that scale to many thousands of nodes• Allow for the storage and analysis of multiple reconciliations for a single gene tree within a single database structure
  7. 7. Extending TR Cyberinfrastructure Generate VisualizeReconciliations Gene Reconciliations Trees TreeBeST primeTV Reconciled primeGSR fltreebest NOTUNG Species Trees annot8r Ontology Functional Annotation
  8. 8. Tree Reconciliation GUI
  9. 9. Tree Reconciliation GUI
  10. 10. Tree Reconciliation GUI
  11. 11. Tree Reconciliation GUI Queries • BLAST • GO Term • Locus Name • Gene Family Name
  12. 12. Current Limitations• Users query against a pre-computed set of reconciliations • We generate the species trees • We generate the gene trees given alignments • We generate reconciliation mappings• Reconciliation visualization is currently tied to the database• Users can NOT submit their own data (genes trees or alignments) for reconciliation
  13. 13. Making TR Phylotastic• Allow users to generate reconciliations using their own data • Supply a species tree OR • Supply an gene family alignment
  14. 14. Phylotastic Components• Name resolution • Given a gene tree or alignments determine the species list• Tree Pruner • Given the species list above, generate the species tree required for reconciliation• NEXML encoding • Return reconciled tree using NEXML
  15. 15. A Phylotastic DNA Subway ..

×