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Gene Tree/ Species Tree Reconciliation Phylotastic Hackathon June 4, 2012

Phylotastic reconciliation

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Author: Jamie Estill

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Page 1: Phylotastic reconciliation

Gene Tree/ Species Tree

Reconciliation

Phylotastic HackathonJune 4, 2012

Page 2: Phylotastic reconciliation

iPlant Tree of Life (iPTOL)

• Tree Reconciliation

• Big Trees

• Data Assembly

• Trait Evolution

• Data Integration

• Tree Visualization

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Gene Tree Reconciliation

Projection of gene trees onto a species tree• gene duplications• gene losses• lineage sorting• horizontal transfer

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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

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Existing TR Cyberinfrastructure

TreeBeST

primeGSR

GenerateReconciliations

primeTV

fltreebest

GeneTrees

EC VisualizeReconciliations

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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

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Ontology

SpeciesTrees

Reconciled

Extending TR Cyberinfrastructure

TreeBeST

primeGSR

GenerateReconciliations

primeTV

fltreebest

GeneTrees

VisualizeReconciliations

annot8r

FunctionalAnnotation

NOTUNG

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Tree Reconciliation GUI

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Tree Reconciliation GUI

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Tree Reconciliation GUI

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Tree Reconciliation GUI

Queries

• BLAST

• GO Term

• Locus Name

• Gene Family Name

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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

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Making TR Phylotastic

• Allow users to generate reconciliations using their own data• Supply a species tree OR• Supply an gene family alignment

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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

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A Phylotastic DNA Subway ..