DeCoSTAR

DeCoSTAR reconstructs ancestral gene and genome organization by reconciling gene trees with species trees to infer duplications, losses, and horizontal transfer events.

Key Features:

• Reconciliation with Phylogenies: Integrates gene tree data with species trees to identify and reconcile discrepancies caused by duplication, loss, and horizontal transfer using reconciled phylogenies.
• Ancestral State Reconstruction: Reconstructs ancestral states by mapping gene family histories onto a species phylogeny to recover ancestral genome organization including duplications, losses, and transfers.
• Comprehensive Evolutionary Analysis: Provides detailed identification of specific duplication, loss, and horizontal transfer events across lineages to characterize genome evolutionary dynamics.

Scientific Applications:

• Evolutionary Biology: Reconstructs ancestral genomes to study the processes that drive genome diversity and complexity across lineages.
• Comparative Genomics: Compares gene families across multiple species to identify conserved elements and divergent evolutionary paths.
• Phylogenetic Studies: Enhances phylogenetic analyses by incorporating gene tree-species tree reconciliation to refine inferred evolutionary relationships and events.

Methodology:

Reconciles gene trees with species trees using algorithms that account for duplication, loss, and horizontal transfer to map gene family histories onto the species phylogeny.