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REvolutionH-tl 2.0: A fast and robust tool for decoding evolutionary gene histories.

José Antonio Ramírez-Rafael·Annachiara Korchmaros·Katia Aviña-Padilla·Alitzel López-Sánchez·Gabriel Martinez-Medina·Alfredo J Hernández-Álvarez·Marc Hellmuth·Peter F Stadler·Maribel Hernández-Rosales
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Abstract

REvolutionH-tl is a fast, scalable, and integrated software platform for inferring orthology relationships, gene trees, species trees, and reconciled evolutionary scenarios directly from sequence data. Built upon the formal framework of best match graphs (BMGs), REvolutionH-tl predicts orthogroups and orthologous gene pairs with high accuracy, requiring neither precomputed trees nor multiple external tools. The software reconstructs event-labeled gene and species trees, seamlessly integrating reconciliation to produce fast, accurate, and biologically insightful evolutionary scenarios. Through extensive benchmarking on synthetic datasets with known ground truth, REvolutionH-tl outperforms or matches the accuracy of established tools such as OrthoFinder, Proteinortho, RAxML, GeneRax, and RANGER-DTL, while achieving significantly lower runtimes. A key innovation of REvolutionH-tl is its built-in support for detailed, publication-ready visualizations, which allow users to explore genome evolution dynamics, orthogroup composition, and reconciliation results with clarity and ease. These visual features position REvolutionH-tl as the first platform of its kind to combine analytical precision with intuitive interpretability. The software is open-source, cross-platform, and freely available at https://pypi.org/project/revolutionhtl/, providing a robust solution for large-scale evolutionary analyses in comparative genomics.

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SoftwareEvolution, MolecularComputational BiologyPhylogenyAlgorithmsGenomicsModels, GeneticDatabases, GeneticJournal ArticleResearch Support, Non-U.S. Gov't

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José Antonio Ramírez-Rafael, Annachiara Korchmaros, Katia Aviña-Padilla, Alitzel López-Sánchez, Gabriel Martinez-Medina, Alfredo J Hernández-Álvarez, Marc Hellmuth, Peter F Stadler, Maribel Hernández-Rosales. 2026-08-12. REvolutionH-tl 2.0: A fast and robust tool for decoding evolutionary gene histories.. https://doi.org/10.1371/journal.pcbi.1013017

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