SylvX

SylvX visualizes phylogenetic reconciliations to compare gene and species trees and highlight evolutionary events such as duplications, transfers, losses, co-speciation, host-switches, and extinctions in host/parasite and gene family studies.

Key Features:

• Classical phylogenetic graphic operators: Implements swapping and highlighting operators to manipulate and emphasize parts of reconciled trees.
• Multiple reconciliation maps: Displays multiple reconciliation maps simultaneously for comparative inspection of alternative reconciliations.
• Sub-reconciliation manipulation: Allows moving and shrinking of sub-reconciliations to manage nested tree structures and focus on substructures.
• Graphical simplification of nested trees: Provides mechanisms to simplify graphical representations of nested gene and species trees to aid interpretation.
• Graph-based representation of events: Represents evolutionary events and their relationships as interconnected graphs within reconciliations.

Scientific Applications:

• Gene family evolution: Visualizes reconciliations to analyze duplications, transfers, and losses shaping gene family histories.
• Host–parasite co-diversification: Elucidates co-speciation events, host-switches, and extinctions in host/parasite evolutionary studies.
• Interpretation of reconciliation outputs: Supports comparative analysis of alternative reconciliations to resolve discrepancies between gene and species trees.

Methodology:

SylvX leverages reconciliation methods to compare gene and species trees, identifies duplications, transfers, and losses, and graphically represents these processes as interconnected graphs using classical operators (swapping, highlighting) and novel visualization techniques (multiple maps, movable and shrinkable sub-reconciliations).