SODA

SODA performs species delimitation using only gene tree topologies to infer species boundaries by testing for zero branch lengths in species trees.

Key Features:

• Gene Tree Topology Utilization: Operates exclusively on gene tree topologies to delimit species.
• Polytomy Test Integration: Incorporates the polytomy test of Sayyari et al., as implemented in the ASTRAL package, to assess zero branch length in species trees.
• Quartet-based Methods: Builds on recent quartet-based methods for species tree inference to leverage their accuracy and scalability.
• Scalability and Speed: Designed to scale to very large datasets and perform analyses efficiently on many gene trees.
• Accuracy Trade-off: Demonstrated high accuracy in simulations while being reported as somewhat less accurate than methods such as BPP in some scenarios.

Scientific Applications:

• Species Delimitation: Delimits species by evaluating gene tree discordance and testing for zero branch lengths to identify species boundaries.
• Species Tree Inference: Aids inference and assessment of species trees from discordant gene trees using quartet-based approaches and polytomy testing.

Methodology:

Operates on gene tree topologies, builds on quartet-based methods, and employs the Sayyari et al. polytomy test (implemented in ASTRAL) to test for zero branch lengths in species trees.