ArticleBioinformatics (Oxford, England)2020
FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- Episode clustering in phylogenetic networks.Bioinformatics (Oxford, England) · 2026Article
- Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.Genome biology and evolution · 2025Article
- AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.Bioinformatics (Oxford, England) · 2024Article
- Unifying duplication episode clustering and gene-species mapping inference.Algorithms for molecular biology : AMB · 2024Article
- Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem.Algorithms for molecular biology : AMB · 2024Article
- wQFM-DISCO: DISCO-enabled wQFM improves phylogenomic analyses despite the presence of paralogs.Bioinformatics advances · 2024Article
- DISCO+QR: rooting species trees in the presence of GDL and ILS.Bioinformatics advances · 2023Article
- Phylogenetic reconciliation.PLoS computational biology · 2022Article
- Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication.Systematic biology · 2022Article
- Recent progress on methods for estimating and updating large phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages.Genome biology and evolution · 2022Article
- Embedding gene trees into phylogenetic networks by conflict resolution algorithms.Algorithms for molecular biology : AMB · 2022Article
- DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition.Systematic biology · 2022Article
- Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs.Systematic biology · 2022Article
- SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss.Molecular biology and evolution · 2022Article
- Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae).Systematic biology · 2021Article
- Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation.Algorithms for molecular biology : AMB · 2021Article
- ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy.Molecular biology and evolution · 2020Article
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2 authors.
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Abstract
motivationSpecies tree estimation is a basic part of biological research but can be challenging because of gene duplication and loss (GDL), which results in genes that can appear more than once in a given genome. All common approaches in phylogenomic studies either reduce available data or are error-prone, and thus, scalable methods that do not discard data and have high accuracy on large heterogeneous datasets are needed.
resultsWe present FastMulRFS, a polynomial-time method for estimating species trees without knowledge of orthology. We prove that FastMulRFS is statistically consistent under a generic model of GDL when adversarial GDL does not occur. Our extensive simulation study shows that FastMulRFS matches the accuracy of MulRF (which tries to solve the same optimization problem) and has better accuracy than prior methods, including ASTRAL-multi (the only method to date that has been proven statistically consistent under GDL), while being much faster than both methods. AVAILABILITY AND IMPEMENTATION: FastMulRFS is available on Github (https://github.com/ekmolloy/fastmulrfs). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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