ArticleBioinformatics (Oxford, England)2015
Joint amalgamation of most parsimonious reconciled gene trees.
Article in Bioinformatics (Oxford, England), 2015. 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.
- Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics.Nature communications · 2024Article
- Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.The ISME journal · 2024Review
- Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.Genome biology and evolution · 2023Article
- virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2.Journal of computational biology : a journal of computational molecular cell biology · 2023Article
- Phylogenetic reconciliation.PLoS computational biology · 2022Article
- Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A Comprehensive Evolutionary Scenario of Cell Division and Associated Processes in the Firmicutes.Molecular biology and evolution · 2021Article
- Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria.Current biology : CB · 2021Article
- 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
- The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models.Journal of mathematical biology · 2020Article
- Tree shape-based approaches for the comparative study of cophylogeny.Ecology and evolution · 2019Article
- Genome size evolution in the Archaea.Emerging topics in life sciences · 2018Article
- Consistency and convergence rate of phylogenetic inference via regularization.Annals of statistics · 2018Article
- Inferring duplication episodes from unrooted gene trees.BMC genomics · 2018Article
- Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family.BMC bioinformatics · 2017Article
- Genome-scale phylogenetic analysis finds extensive gene transfer among fungi.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2015Article
- Reconstructing a SuperGeneTree minimizing reconciliation.BMC bioinformatics · 2015Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationTraditionally, gene phylogenies have been reconstructed solely on the basis of molecular sequences; this, however, often does not provide enough information to distinguish between statistically equivalent relationships. To address this problem, several recent methods have incorporated information on the species phylogeny in gene tree reconstruction, leading to dramatic improvements in accuracy. Although probabilistic methods are able to estimate all model parameters but are computationally expensive, parsimony methods-generally computationally more efficient-require a prior estimate of parameters and of the statistical support.
resultsHere, we present the Tree Estimation using Reconciliation (TERA) algorithm, a parsimony based, species tree aware method for gene tree reconstruction based on a scoring scheme combining duplication, transfer and loss costs with an estimate of the sequence likelihood. TERA explores all reconciled gene trees that can be amalgamated from a sample of gene trees. Using a large scale simulated dataset, we demonstrate that TERA achieves the same accuracy as the corresponding probabilistic method while being faster, and outperforms other parsimony-based methods in both accuracy and speed. Running TERA on a set of 1099 homologous gene families from complete cyanobacterial genomes, we find that incorporating knowledge of the species tree results in a two thirds reduction in the number of apparent transfer events.
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