ArticlePloS one2016
Efficient Gene Tree Correction Guided by Genome Evolution.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- A Group 6 LEA Protein Plays Key Roles in Tolerance to Water Deficit, and in Maintaining the Glassy State and Longevity of Seeds.Plant, cell & environment · 2025Article
- "Correcting" Gene Trees to be More Like Species Trees Frequently Increases Topological Error.Genome biology and evolution · 2023Article
- An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication.Genome research · 2022Article
- Article
- ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy.Molecular biology and evolution · 2020Article
- GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene Family Tree Inference under Gene Duplication, Transfer, and Loss.Molecular biology and evolution · 2020Article
- Novel phylogenetic methods are needed for understanding gene function in the era of mega-scale genome sequencing.Nucleic acids research · 2020Article
- A Screen for Gene Paralogies Delineating Evolutionary Branching Order of Early Metazoa.G3 (Bethesda, Md.) · 2020Article
- Non-parametric correction of estimated gene trees using TRACTION.Algorithms for molecular biology : AMB · 2020Article
- Advances and Applications in the Quest for Orthologs.Molecular biology and evolution · 2019Article
- Evolutionary Relationships Between the Laccase Genes of Polyporales: Orthology-Based Classification of Laccase Isozymes and Functional Insight FromFrontiers in microbiology · 2019Article
- RecPhyloXML: a format for reconciled gene trees.Bioinformatics (Oxford, England) · 2018Article
- Revised Phylogeny of thePlant physiology · 2018Article
- Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.BMC genomics · 2018Article
- GATC: a genetic algorithm for gene tree construction under the Duplication-Transfer-Loss model of evolution.BMC genomics · 2018Article
- Inferring duplication episodes from unrooted gene trees.BMC genomics · 2018Article
- Gene tree parsimony for incomplete gene trees: addressing true biological loss.Algorithms for molecular biology : AMB · 2018Article
- OCTAL: Optimal Completion of gene trees in polynomial time.Algorithms for molecular biology : AMB · 2018Article
- DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies.Genome biology and evolution · 2017Article
- Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationsGene trees inferred solely from multiple alignments of homologous sequences often contain weakly supported and uncertain branches. Information for their full resolution may lie in the dependency between gene families and their genomic context. Integrative methods, using species tree information in addition to sequence information, often rely on a computationally intensive tree space search which forecloses an application to large genomic databases.
resultsWe propose a new method, called ProfileNJ, that takes a gene tree with statistical supports on its branches, and corrects its weakly supported parts by using a combination of information from a species tree and a distance matrix. Its low running time enabled us to use it on the whole Ensembl Compara database, for which we propose an alternative, arguably more plausible set of gene trees. This allowed us to perform a genome-wide analysis of duplication and loss patterns on the history of 63 eukaryote species, and predict ancestral gene content and order for all ancestors along the phylogeny. AVAILABILITY: A web interface called RefineTree, including ProfileNJ as well as a other gene tree correction methods, which we also test on the Ensembl gene families, is available at: http://www-ens.iro.umontreal.ca/~adbit/polytomysolver.html. The code of ProfileNJ as well as the set of gene trees corrected by ProfileNJ from Ensembl Compara version 73 families are also made available.
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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.