GeneRax

GeneRax infers species-tree-aware, maximum-likelihood gene trees by integrating sequence substitutions and gene-level events (duplication, transfer, loss) to model gene family evolution.

Key Features:

• Species Tree-Aware Inference: Leverages information from a putative species tree to improve phylogenetic inference for individual homologous gene families.
• Maximum Likelihood Framework: Employs full likelihood optimization to infer gene trees under an explicit probabilistic model.
• Comprehensive Event Modeling: Simultaneously accounts for sequence substitutions and gene-level events—duplication, transfer, and loss—within the inference framework.
• Parallelization: Supports parallel execution for large-scale analyses, demonstrated by completing tree inferences and reconciliations for 1,099 Cyanobacteria families in eight minutes using 512 CPU cores.
• Performance: Empirical evaluations report it as the fastest method among tested approaches starting from aligned sequences and consistently producing the highest likelihood scores under its model, with simulations showing approximately 90% accuracy relative to true trees by relative Robinson–Foulds distance.

Scientific Applications:

• Modeling gene family evolution across species: Reconstruction of rooted gene trees that incorporate duplication, transfer, and loss for comparative genomics and evolutionary biology studies.

Methodology:

Directly infers rooted phylogenetic trees from per-gene sequence alignments and a rooted, undated species tree, avoiding computation of bootstrap trees and not relying on approximations or heuristics that limit exploration of tree space.