Triplet-based species tree estimation: Sensitivity to gene tree rooting (or lack thereof).

Triplet-based species tree estimation with STELAR is generally robust to gene tree rooting, matching or surpassing quartet methods like ASTRAL under various conditions.

• Why it matters: Accurate species tree inference is hindered by gene tree heterogeneity and the challenge of correctly rooting gene trees, which impacts triplet-based methods' reliability in phylogenomics.
• What they did: The study conducted an extensive empirical analysis of multiple gene tree rooting strategies across simulated and real datasets, evaluating their effects on triplet-based species tree inference with STELAR.
• The result: Findings show that triplet-based methods can perform well even with unrooted gene trees, offering insights into their utility and guiding better rooting practices for phylogenomic analyses.