ArticleAlgorithms for molecular biology : AMB2020
Reconstruction of time-consistent species trees.
Article in Algorithms for molecular biology : AMB, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Predicting horizontal gene transfers with perfect transfer networks.Algorithms for molecular biology : AMB · 2024Article
- Relative timing information and orthology in evolutionary scenarios.Algorithms for molecular biology : AMB · 2023Article
- Indirect identification of horizontal gene transfer.Journal of mathematical biology · 2021Article
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2 authors.
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Abstract
backgroundThe history of gene families-which are equivalent to event-labeled gene trees-can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The question then arises as whether inferred event-labeled gene trees are "biologically feasible" which is the case if one can find a species tree with which the gene tree can be reconciled in a time-consistent way.
resultsIn this contribution, we consider event-labeled gene trees that contain speciations, duplications as well as horizontal gene transfer (HGT) and we assume that the species tree is unknown. Although many problems become NP-hard as soon as HGT and time-consistency are involved, we show, in contrast, that the problem of finding a time-consistent species tree for a given event-labeled gene can be solved in polynomial-time. We provide a cubic-time algorithm to decide whether a "time-consistent" species tree for a given event-labeled gene tree exists and, in the affirmative case, to construct the species tree within the same time-complexity.
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