Xscape

Xscape performs phylogenetic tree reconciliation under the Duplication-Loss-Transfer (DLT) model using a maximum parsimony approach for undated trees.

Key Features:

• Maximum Parsimony Reconciliation: Implements a maximum parsimony framework that assigns costs to duplications, losses, and transfers and finds reconciliations with minimum total cost.
• Sensitivity Analysis of Event Costs: Computes Pareto-optimal sets of reconciliations across different event-cost assignments to assess sensitivity to cost choices.
• Cophylogenetic Analyses: Provides statistical tests and computes event support values for cophylogenetic inference, including host–parasite comparisons.
• Support for Undated Trees: Operates on undated phylogenetic trees.
• Versatile Applications: Applies to gene trees versus species trees, parasite versus host trees, and species trees versus area cladograms.

Scientific Applications:

• Gene family evolution: Reconstructs duplication, loss, and transfer histories for studies of gene-family evolution.
• Host–parasite co-evolution: Tests and quantifies co-evolutionary scenarios in host–parasite systems using cophylogenetic reconciliation and event support.
• Biogeography (area cladograms): Analyzes species trees versus area cladograms to infer events relevant to biogeographic history.
• Comparative analyses of interdependent entities: Investigates evolutionary relationships among other interdependent biological entities through reconciliations under the DLT model.

Methodology:

Uses a maximum parsimony approach within the Duplication-Loss-Transfer (DLT) model by assigning costs to duplications, losses, and transfers and minimizing total cost; computes Pareto-optimal sets of reconciliations for sensitivity analysis; applies statistical tests and computes event support values; operates on undated trees.