ArticleBMC bioinformatics2013
Gene tree correction guided by orthology.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy.Molecular biology and evolution · 2020Article
- Non-parametric correction of estimated gene trees using TRACTION.Algorithms for molecular biology : AMB · 2020Article
- Evolutionary Relationships Between the Laccase Genes of Polyporales: Orthology-Based Classification of Laccase Isozymes and Functional Insight FromFrontiers in microbiology · 2019Article
- Reconstructing gene trees from Fitch's xenology relation.Journal of mathematical biology · 2018Article
- Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species.BMC bioinformatics · 2017Article
- Approximating the correction of weighted and unweighted orthology and paralogy relations.Algorithms for molecular biology : AMB · 2017Article
- Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies.BMC genomics · 2016Article
- Efficient Gene Tree Correction Guided by Genome Evolution.PloS one · 2016Article
- The link between orthology relations and gene trees: a correction perspective.Algorithms for molecular biology : AMB · 2016Article
- The inference of gene trees with species trees.Systematic biology · 2015Review
- Polytomy refinement for the correction of dubious duplications in gene trees.Bioinformatics (Oxford, England) · 2014Article
- Orthology and paralogy constraints: satisfiability and consistency.BMC genomics · 2014Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundReconciled gene trees yield orthology and paralogy relationships between genes. This information may however contradict other information on orthology and paralogy provided by other footprints of evolution, such as conserved synteny.
resultsWe explore a way to include external information on orthology in the process of gene tree construction. Given an initial gene tree and a set of orthology constraints on pairs of genes or on clades, we give polynomial-time algorithms for producing a modified gene tree satisfying the set of constraints, that is as close as possible to the original one according to the Robinson-Foulds distance. We assess the validity of the modifications we propose by computing the likelihood ratio between initial and modified trees according to sequence alignments on Ensembl trees, showing that often the two trees are statistically equivalent. AVAILABILITY: Software and data available upon request to the corresponding author.
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Registered trials
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.