ArticleBioinformatics (Oxford, England)2017
FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Integrating phylogenies with chronology to assemble the tree of life.Frontiers in bioinformatics · 2025Article
- Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem.Algorithms for molecular biology : AMB · 2024Article
- Spectral cluster supertree: fast and statistically robust merging of rooted phylogenetic trees.Frontiers in molecular biosciences · 2024Article
- Weighted ASTRID: fast and accurate species trees from weighted internode distances.Algorithms for molecular biology : AMB · 2023Article
- Article
- Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data.Bioinformatics (Oxford, England) · 2023Article
- DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition.Systematic biology · 2022Article
- Article
- Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation.Algorithms for molecular biology : AMB · 2021Article
- FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models.Bioinformatics (Oxford, England) · 2020Article
- Forcing external constraints on tree inference using ASTRAL.BMC genomics · 2020Article
- Linear-time algorithms for phylogenetic tree completion under Robinson-Foulds distance.Algorithms for molecular biology : AMB · 2020Article
- The performance of coalescent-based species tree estimation methods under models of missing data.BMC genomics · 2018Article
- SIESTA: enhancing searches for optimal supertrees and species trees.BMC genomics · 2018Article
- Gene tree parsimony for incomplete gene trees: addressing true biological loss.Algorithms for molecular biology : AMB · 2018Article
- BCD Beam Search: considering suboptimal partial solutions in Bad Clade Deletion supertrees.PeerJ · 2018Article
- Bad Clade Deletion Supertrees: A Fast and Accurate Supertree Algorithm.Molecular biology and evolution · 2017Article
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2 authors.
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Abstract
Motivation: The estimation of phylogenetic trees is a major part of many biological dataset analyses, but maximum likelihood approaches are NP-hard and Bayesian MCMC methods do not scale well to even moderate-sized datasets. Supertree methods, which are used to construct trees from trees computed on subsets, are critically important tools for enabling the statistical estimation of phylogenies for large and potentially heterogeneous datasets. Supertree estimation is itself NP-hard, and no current supertree method has sufficient accuracy and scalability to provide good accuracy on the large datasets that supertree methods were designed for, containing thousands of species and many subset trees. Results: We present FastRFS, a new method based on a dynamic programming method we have developed to find an exact solution to the Robinson-Foulds Supertree problem within a constrained search space. FastRFS has excellent accuracy in terms of criterion scores and topological accuracy of the resultant trees, substantially improving on competing methods on a large collection of biological and simulated data. In addition, FastRFS is extremely fast, finishing in minutes on even very large datasets, and in under an hour on a biological dataset with 2228 species. Availability and Implementation: FastRFS is available on github at https://github.com/pranjalv123/FastRFS. Contact: warnow@illinois.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
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