SOI

SOI leverages the Orthology Index (OI) to identify orthologous synteny with scalable and reliable analysis, enabling accurate reconstruction of evolutionary history in cases with polyploidy.

Key Features:

• Orthology Index (OI): A scalable and robust metric for identifying orthologous synteny that effectively distinguishes orthologous from out-paralogous synteny.
• Polyploidy handling: Reliable performance across diverse polyploidization events and varied polyploidy histories.
• Simulation-based validation: Benchmarking demonstrates superior accuracy compared to existing methods across a wide range of scenarios.

Scientific Applications:

• Polyploidy inference: Detection of whole-genome duplication events in plant evolutionary history.
• Reticulation identification: Detection of hybridization and network evolutionary patterns in plant genomes.
• Phylogenomics: Reconstruction of evolutionary histories and relationships from whole-genome datasets.

Methodology:

SOI is based on the Orthology Index (OI), a quantitative approach for identifying orthologous synteny; evaluation was performed on large-scale empirical datasets with diverse polyploidization events and through simulation-based benchmarks.