ArticleAlgorithms for molecular biology : AMB2018
Gene tree parsimony for incomplete gene trees: addressing true biological loss.
Article in Algorithms for molecular biology : AMB, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Leveraging Weighted Quartet Distributions for Enhanced Species Tree Inference from Genome-Wide Data.Genome biology and evolution · 2025Article
- Terraces in species tree inference from gene trees.BMC ecology and evolution · 2024Article
- Challenges in Assembling the Dated Tree of Life.Genome biology and evolution · 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
- 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
- FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models.Bioinformatics (Oxford, England) · 2020Article
- STELAR: a statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency.BMC genomics · 2020Article
- TreeMerge: a new method for improving the scalability of species tree estimation methods.Bioinformatics (Oxford, England) · 2019Article
- A customized nuclear target enrichment approach for developing a phylogenomic baseline forApplications in plant sciences · 2019Article
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2 authors.
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Abstract
motivationSpecies tree estimation from gene trees can be complicated by gene duplication and loss, and "gene tree parsimony" (GTP) is one approach for estimating species trees from multiple gene trees. In its standard formulation, the objective is to find a species tree that minimizes the total number of gene duplications and losses with respect to the input set of gene trees. Although much is known about GTP, little is known about how to treat inputs containing some
resultsWe present new theory for GTP considering whether the incompleteness is due to gene birth and death (i.e., true biological loss) or taxon sampling, and present dynamic programming algorithms that can be used for an exact but exponential time solution for small numbers of taxa, or as a heuristic for larger numbers of taxa. We also prove that the "standard" calculations for duplications and losses exactly solve GTP when incompleteness results from taxon sampling, although they can be incorrect when incompleteness results from true biological loss. The software for the DP algorithm is freely available as open source code at https://github.com/smirarab/DynaDup.
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