ArticlePloS one2010
A benchmark of parametric methods for horizontal transfers detection.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- On the Low Abundance of Antibiotic Resistance Genes in Bacteriophage Genomes and Their Random Acquisition via Specialized Transduction.Genome biology and evolution · 2026Article
- What impact do new homologs have on detecting interdomain horizontal gene transfer in eukaryotes? A reassessment of Katz (2015).Biology open · 2026Article
- Genomic data representations for horizontal gene transfer detection.NAR genomics and bioinformatics · 2025Article
- Horizontal Gene Transfer Inference: Gene Presence-Absence Outperforms Gene Trees.Molecular biology and evolution · 2025Article
- Profiling lateral gene transfer events in the human microbiome using WAAFLE.Nature microbiology · 2025Article
- The Fur-like regulatory protein MAP3773c modulates key metabolic pathways in Mycobacterium avium subsp. paratuberculosis under in-vitro iron starvation.Scientific reports · 2024Article
- The Theory of Gene Family Histories.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Evolution of the connectivity and indispensability of a transferable gene: the simplicity hypothesis.BMC ecology and evolution · 2022Article
- Indirect identification of horizontal gene transfer.Journal of mathematical biology · 2021Article
- Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin.BMC ecology and evolution · 2021Article
- Rewiring the specificity of extracytoplasmic function sigma factors.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
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- Genomic Analysis ofG3 (Bethesda, Md.) · 2019Article
- Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation.Scientific reports · 2019Article
- Alignment-free inference of hierarchical and reticulate phylogenomic relationships.Briefings in bioinformatics · 2019Review
- Alignment-Free Sequence Analysis and Applications.Annual review of biomedical data science · 2018Article
- Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer.Frontiers in microbiology · 2018Article
- Evolutionary History of Copper Membrane Monooxygenases.Frontiers in microbiology · 2018Article
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3 authors.
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Abstract
Horizontal gene transfer (HGT) has appeared to be of importance for prokaryotic species evolution. As a consequence numerous parametric methods, using only the information embedded in the genomes, have been designed to detect HGTs. Numerous reports of incongruencies in results of the different methods applied to the same genomes were published. The use of artificial genomes in which all HGT parameters are controlled allows testing different methods in the same conditions. The results of this benchmark concerning 16 representative parametric methods showed a great variety of efficiencies. Some methods work very poorly whatever the type of HGTs and some depend on the conditions or on the metrics used. The best methods in terms of total errors were those using tetranucleotides as criterion for the window methods or those using codon usage for gene based methods and the Kullback-Leibler divergence metric. Window methods are very sensitive but less specific and detect badly lone isolated gene. On the other hand gene based methods are often very specific but lack of sensitivity. We propose using two methods in combination to get the best of each category, a gene based one for specificity and a window based one for sensitivity.
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