phylotastic reconciliation
DESCRIPTION
Author: Jamie EstillTRANSCRIPT
Gene Tree/ Species Tree
Reconciliation
Phylotastic HackathonJune 4, 2012
iPlant Tree of Life (iPTOL)
• Tree Reconciliation
• Big Trees
• Data Assembly
• Trait Evolution
• Data Integration
• Tree Visualization
Gene Tree Reconciliation
Projection of gene trees onto a species tree• gene duplications• gene losses• lineage sorting• horizontal transfer
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
Existing TR Cyberinfrastructure
TreeBeST
primeGSR
GenerateReconciliations
primeTV
fltreebest
GeneTrees
EC VisualizeReconciliations
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
Ontology
SpeciesTrees
Reconciled
Extending TR Cyberinfrastructure
TreeBeST
primeGSR
GenerateReconciliations
primeTV
fltreebest
GeneTrees
VisualizeReconciliations
annot8r
FunctionalAnnotation
NOTUNG
Tree Reconciliation GUI
Tree Reconciliation GUI
Tree Reconciliation GUI
Tree Reconciliation GUI
Queries
• BLAST
• GO Term
• Locus Name
• Gene Family Name
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
Making TR Phylotastic
• Allow users to generate reconciliations using their own data• Supply a species tree OR• Supply an gene family alignment
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
A Phylotastic DNA Subway ..