QuartetScores

QuartetScores quantifies phylogenetic incongruence by computing quartet-based internode certainty (IC) measures for complete and partial phylogenetic trees.

Key Features:

• Quartet-based IC measures: Implements three IC measures derived from quartet frequencies applicable to both complete and partial phylogenetic trees.
• Robustness to missing taxa: Quartet-based measures maintain consistent IC scores across datasets with high proportions of missing taxa, avoiding the overestimation observed with some bipartition-based approaches.
• Error resilience: Exhibits greater robustness to errors in phylogenetic inference and to absence of phylogenetic signal.
• Handling of partial gene trees: Accommodates incomplete gene trees without requiring adjustments to bipartition frequencies from partial gene trees.

Scientific Applications:

• Phylogenomic incongruence analysis: Provides more accurate internode certainty estimates to identify and characterize topological conflict within internal branches of phylogenetic trees, particularly when data partitions (e.g., genes) have missing taxa.
• Benchmarking of IC measures: Enables comparison with bipartition-based IC measures on simulated datasets and mammalian phylogenomic data, showing similar scores for complete datasets and more consistent scores across varying levels of missing taxa.

Methodology:

Calculates IC by analyzing quartet frequencies and implements three quartet-frequency–based IC measures applicable to complete and partial trees; this quartet-based approach inherently accommodates incomplete datasets without modifying bipartition frequencies as done in bipartition-based methods.