REvolutionH-tl

REvolutionH-tl infers orthology relationships, gene trees, species trees, and reconciled evolutionary scenarios directly from sequence data using the formal framework of best match graphs (BMGs).

Key Features:

• Orthogroup prediction: Predicts orthogroups and orthologous gene pairs with high accuracy without requiring precomputed trees or multiple external tools.
• Gene tree reconstruction: Reconstructs event-labeled gene trees from sequence data.
• Species tree inference: Reconstructs species trees as part of the integrated evolutionary analysis workflow.
• Tree reconciliation: Seamlessly integrates reconciliation of gene and species trees to produce event-labeled evolutionary scenarios.
• Visualization: Generates detailed, publication-ready visualizations of genome evolution dynamics, orthogroup composition, and reconciliation results.
• Benchmarking performance: Outperforms or matches the accuracy of OrthoFinder, Proteinortho, RAxML, GeneRax, and RANGER-DTL on synthetic datasets with known ground truth while achieving significantly lower runtimes.

Scientific Applications:

• Comparative genomics: Enables large-scale evolutionary analyses to study genome evolution across species.
• Orthology assignment: Identifies groups of related genes and orthologous gene pairs for evolutionary and functional studies.
• Evolutionary scenario reconstruction: Produces biologically insightful reconciled evolutionary scenarios including gene duplications and losses.

Methodology:

REvolutionH-tl is built upon the formal framework of best match graphs (BMGs) and automates the entire evolutionary reconstruction process starting from protein sequences.