ArticleBriefings in bioinformatics2023
HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic Review: Long-Read Sequencing in Algal Studies.International journal of molecular sciences · 2026Pooled it
- Safety and Next-Generation Probiotic Potential of Mitsuokella multacida AGMB01124 Newly Isolated from Healthy Swine Feces.Probiotics and antimicrobial proteins · 2026Article
- Unique Tunicate Traits Possibly Encoded by Horizontally Transferred Genes.Genome biology and evolution · 2026Article
- Distinct genomic trajectory among invasive Salmonella Typhimurium ST313 infections.Nature communications · 2026Article
- Plant recognition by Trichoderma Harzianum elicits upregulation of a novel secondary metabolite cluster required for colonization.Scientific reports · 2026Article
- The genome of Pleurosigma provides insights into the evolutionary adaptations of pelagic diatoms.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Jumbo phage-mediated transduction of genomic islands.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes.Molecular biology and evolution · 2025Article
- Mosaic Evolution of Membrane Transporters in Galdieriales.Plants (Basel, Switzerland) · 2025Article
- Multiple Horizontal Transfers of Immune Genes Between Distantly Related Teleost Fishes.Molecular biology and evolution · 2025Article
- Avian-specificeLife · 2025Article
- Article
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Authors and funding
5 authors.
Funding
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Abstract
backgroundHorizontal gene transfer (HGT) is an important driver in genome evolution, gain-of-function, and metabolic adaptation to environmental niches. Genome-wide identification of putative HGT events has become increasingly practical, given the rapid growth of genomic data. However, existing HGT analysis toolboxes are not widely used, limited by their inability to perform phylogenetic reconstruction to explore potential donors, and the detection of HGT from both evolutionarily distant and closely related species.
resultsIn this study, we have developed HGTphyloDetect, which is a versatile computational toolbox that combines high-throughput analysis with phylogenetic inference, to facilitate comprehensive investigation of HGT events. Two case studies with Saccharomyces cerevisiae and Candida versatilis demonstrate the ability of HGTphyloDetect to identify horizontally acquired genes with high accuracy. In addition, HGTphyloDetect enables phylogenetic analysis to illustrate a likely path of gene transmission among the evolutionarily distant or closely related species.
conclusionsThe HGTphyloDetect computational toolbox is designed for ease of use and can accurately find HGT events with a very low false discovery rate in a high-throughput manner. The HGTphyloDetect toolbox and its related user tutorial are freely available at https://github.com/SysBioChalmers/HGTphyloDetect.
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