DoubleRecViz

DoubleRecViz visualizes triple-level phylogenetic tree reconciliations to explore co-evolutionary relationships among transcripts, genes, and species.

Key Features:

• Triple-Level Reconciliation Visualization: Visualizes joint reconciliations across transcript, gene, and species levels by displaying reconciled gene trees within species trees and reconciled transcript trees within gene trees.
• Annotation Capabilities: Annotates tree nodes with information corresponding to underlying co-evolutionary events.
• Extended RecPhyloXML Model: Extends the RecPhyloXML model to represent joint transcript-gene and gene-species reconciliations.

Scientific Applications:

• Parasite-Host Co-evolution: Maps phylogenetic relationships across transcripts, genes, and species to investigate parasite-host co-evolution.
• Gene-Species Co-evolution: Explores evolutionary relationships between genes and their corresponding species.
• Transcript-Gene-Species Co-evolution: Investigates co-evolutionary dynamics among transcripts, genes, and species.

Methodology:

Extends the RecPhyloXML model to represent joint transcript-gene and gene-species reconciliations, visualizes reconciled gene trees embedded within species trees and transcript trees nested within gene trees, and annotates tree nodes with inferred co-evolutionary events.