ArticleBioinformatics (Oxford, England)2023
syntenet: an R/Bioconductor package for the inference and analysis of synteny networks.
Article in Bioinformatics (Oxford, England), 2023. 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.
- Near chromosome-level genome assembly of Neomusotima conspurcatalis gives insights into the evolution of moth genome architecture and fern-insect interactions.G3 (Bethesda, Md.) · 2026Article
- Phylogenomic Insights into High Conservation and Lineage-Specific Expansion of the ABAPT Gene Family in Plants.International journal of molecular sciences · 2026Article
- Phylogenomic synteny reveals paleohexaploid-derived genomic blocks across Asteraceae.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Stable genome structures in living fossil fishes.Genome research · 2026Article
- Genomic-Driven Identification of Conserved Biosynthetic Gene Clusters inMetabolites · 2026Article
- PGDD 2.0: Plant Genome Duplication Database with updated content and tools.Nucleic acids research · 2026Article
- Bioinformatics in crop research: using genomic data for crop improvement.Frontiers in plant science · 2026Review
- Comparative Genomics Using GeneDiscoveR: A Toolbox for the Identification of Gene Candidates Associated with Plant Traits.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Comprehensive Annotation of Olfactory and Gustatory Receptor Genes and Transposable Elements Revealed Their Evolutionary Dynamics in Aphids.Molecular biology and evolution · 2025Article
- Genome Architecture and Speciation in Plants and Animals.Molecular ecology · 2025Review
- Construction of Ancestral Chromosomes in Gymnosperms and the Application in Comparative Genomic Analysis.Plants (Basel, Switzerland) · 2025Article
- Article
- Oryza genome evolution through a tetraploid lens.Nature genetics · 2025Article
- Multiple Retrotransposon-mediated NF-YA Gene Duplication Events Recurred in Diverse Groups of Mammals at Different Ancestry Levels.Genome biology and evolution · 2025Article
- doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.Bioinformatics (Oxford, England) · 2025Article
- Genomic and Transcriptomic Insights into the Evolution of C4 Photosynthesis in Grasses.Genome biology and evolution · 2024Article
- The promise and pitfalls of synteny in phylogenomics.PLoS biology · 2024Article
- The chromosome-level genome of the submerged plant Cryptocoryne crispatula provides insights into the terrestrial-freshwater transition in Araceae.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Tracking the Diversity and Chromosomal Distribution of the Olfactory Receptor Gene Repertoires of Three Anurans Species.Journal of molecular evolution · 2023Article
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Authors and funding
5 authors.
Funding
Abstract
summaryInterpreting and visualizing synteny relationships across several genomes is a challenging task. We previously proposed a network-based approach for better visualization and interpretation of large-scale microsynteny analyses. Here, we present syntenet, an R package to infer and analyze synteny networks from whole-genome protein sequence data. The package offers a simple and complete framework, including data preprocessing, synteny detection and network inference, network clustering and phylogenomic profiling, and microsynteny-based phylogeny inference. Graphical functions are also available to create publication-ready plots. Synteny networks inferred with syntenet can highlight taxon-specific gene clusters that likely contributed to the evolution of important traits, and microsynteny-based phylogenies can help resolve phylogenetic relationships under debate. AVAILABILITY AND IMPLEMENTATION: syntenet is available on Bioconductor (https://bioconductor.org/packages/syntenet), and the source code is available on a GitHub repository (https://github.com/almeidasilvaf/syntenet). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.