phylotastic reconciliation

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 ..