ArticleBioinformatics (Oxford, England)2022
NetRAX: accurate and fast maximum likelihood phylogenetic network inference.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Algebraic Invariants for Inferring 4-Leaf Semi-Directed Phylogenetic Networks.Systematic biology · 2026Article
- Do syngameons exist in tropical trees? Challenges to determine their existence and estimate their frequency.Biology letters · 2025Review
- Ancient Introgression Explains Mitochondrial Genome Capture and Mitonuclear Discordance Among South American Collared Tropidurus Lizards.Molecular ecology · 2025Article
- Phylogenetic networks empower biodiversity research.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Leveraging graphical model techniques to study evolution on phylogenetic networks.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline.Systematic biology · 2024Article
- Phylogenomics and plastome evolution of Lithospermeae (Boraginaceae).BMC plant biology · 2024Article
- Anomalous networks under the multispecies coalescent: theory and prevalence.Journal of mathematical biology · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- ANOMALOUS NETWORKS UNDER THE MULTISPECIES COALESCENT: THEORY AND PREVALENCE.bioRxiv : the preprint server for biology · 2023Article
- A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings.Genome research · 2023Article
- Recent progress on methods for estimating and updating large phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- Classes of explicit phylogenetic networks and their biological and mathematical significance.Journal of mathematical biology · 2022Review
- Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum.American journal of botany · 2022Article
- SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss.Molecular biology and evolution · 2022Article
- SPLACE: A tool to automatically SPLit, Align, and ConcatenatE genes for phylogenomic inference of several organisms.Frontiers in bioinformatics · 2022Article
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5 authors.
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Abstract
motivationPhylogenetic networks can represent non-treelike evolutionary scenarios. Current, actively developed approaches for phylogenetic network inference jointly account for non-treelike evolution and incomplete lineage sorting (ILS). Unfortunately, this induces a very high computational complexity and current tools can only analyze small datasets.
resultsWe present NetRAX, a tool for maximum likelihood (ML) inference of phylogenetic networks in the absence of ILS. Our tool leverages state-of-the-art methods for efficiently computing the phylogenetic likelihood function on trees, and extends them to phylogenetic networks via the notion of 'displayed trees'. NetRAX can infer ML phylogenetic networks from partitioned multiple sequence alignments and returns the inferred networks in Extended Newick format. On simulated data, our results show a very low relative difference in Bayesian Information Criterion (BIC) score and a near-zero unrooted softwired cluster distance to the true, simulated networks. With NetRAX, a network inference on a partitioned alignment with 8000 sites, 30 taxa and 3 reticulations completes within a few minutes on a standard laptop. AVAILABILITY AND IMPLEMENTATION: Our implementation is available under the GNU General Public License v3.0 at https://github.com/lutteropp/NetRAX. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.