RecPhyloXML

RecPhyloXML specifies a standardized XML format to annotate gene tree–species tree reconciliations with evolutionary events such as speciation, gene duplication, horizontal transfer, and loss.

Key Features:

• Standardized format: Provides an integrative XML specification for representing phylogenetic reconciliations across different algorithms and software.
• Event annotation: Encodes detailed evolutionary events on gene tree nodes, including speciation, gene duplication, horizontal transfer, and loss.
• Species tree mapping: Represents mappings of gene tree nodes onto species trees and accommodates both dated and undated species trees.

Scientific Applications:

• Comparative analysis: Enables direct comparison of reconciliation outputs produced by different reconciliation algorithms and software.
• Data integration: Facilitates integration and exchange of reconciliation data across tools and workflows.
• Reproducibility: Provides a common serialized format for storing reconciliation annotations to support reproducible analyses.

Methodology:

Reconciliations are represented by annotating gene tree nodes with evolutionary events (speciation, duplication, horizontal transfer, loss) and mapping those nodes onto a species tree, with support for dated and undated species trees.