ArticleBMC genomics2014
Orthology and paralogy constraints: satisfiability and consistency.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Article
- 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
- Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs.Journal of mathematical biology · 2021Article
- A generalized Robinson-Foulds distance for labeled trees.BMC genomics · 2020Article
- Best match graphs and reconciliation of gene trees with species trees.Journal of mathematical biology · 2020Article
- Reconciling event-labeled gene trees with MUL-trees and species networks.Journal of mathematical biology · 2019Article
- Best match graphs.Journal of mathematical biology · 2019Article
- Reconstructing gene trees from Fitch's xenology relation.Journal of mathematical biology · 2018Article
- Accurate prediction of orthologs in the presence of divergence after duplication.Bioinformatics (Oxford, England) · 2018Article
- Inferring phylogenetic trees from the knowledge of rare evolutionary events.Journal of mathematical biology · 2018Article
- Time-consistent reconciliation maps and forbidden time travel.Algorithms for molecular biology : AMB · 2018Article
- Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference.Bioinformatics (Oxford, England) · 2017Article
- Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species.BMC bioinformatics · 2017Article
- Biologically feasible gene trees, reconciliation maps and informative triples.Algorithms for molecular biology : AMB · 2017Article
- Approximating the correction of weighted and unweighted orthology and paralogy relations.Algorithms for molecular biology : AMB · 2017Article
- On the consistency of orthology relationships.BMC bioinformatics · 2016Article
- Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies.BMC genomics · 2016Article
- The link between orthology relations and gene trees: a correction perspective.Algorithms for molecular biology : AMB · 2016Article
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2 authors.
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Abstract
backgroundA variety of methods based on sequence similarity, reconciliation, synteny or functional characteristics, can be used to infer orthology and paralogy relations between genes of a given gene family G. But is a given set C of orthology/paralogy constraints possible, i.e., can they simultaneously co-exist in an evolutionary history for G? While previous studies have focused on full sets of constraints, here we consider the general case where C does not necessarily involve a constraint for each pair of genes. The problem is subdivided in two parts: (1) Is C satisfiable, i.e. can we find an event-labeled gene tree G inducing C? (2) Is there such a G which is consistent, i.e., such that all displayed triplet phylogenies are included in a species tree?
resultsPrevious results on the Graph sandwich problem can be used to answer to (1), and we provide polynomial-time algorithms for satisfiability and consistency with a given species tree. We also describe a new polynomial-time algorithm for the case of consistency with an unknown species tree and full knowledge of pairwise orthology/paralogy relationships, as well as a branch-and-bound algorithm in the case when unknown relations are present. We show that our algorithms can be used in combination with ProteinOrtho, a sequence similarity-based orthology detection tool, to extract a set of robust orthology/paralogy relationships.
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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.