Treerecs

Treerecs reconciles gene trees with species trees using a duplication–loss model to infer gene duplication and loss events and align gene evolutionary histories with species phylogenies.

Key Features:

• Duplication-Loss Reconciliation: Implements a duplication–loss model to reconcile gene trees with species trees and infer duplication and loss events.
• Performance and Versatility: Noted for speed and versatility, enabling efficient processing of diverse phylogenetic analyses.
• Graphical Output: Produces graphical representations of reconciled trees for visualization of evolutionary relationships.
• Integration with Phylogenetic Inference Methods: Integrates with phylogenetic inference methods on multiple alignments, such as PLL and Seaview.

Scientific Applications:

• Evolutionary history reconstruction: Reconstructs the evolutionary histories of genes and species by reconciling gene and species trees.
• Error detection in gene trees: Identifies potential errors or inconsistencies in gene tree construction arising from limited data by aligning gene trees to species phylogenies.
• Phylogenetic model refinement: Supports refinement of phylogenetic models through reconciliation-informed correction of gene tree discrepancies.

Methodology:

Implements a duplication–loss reconciliation approach that accounts for gene duplications and losses to align gene trees with species trees.