ArticleMicrobial genomics2018
SynerClust: a highly scalable, synteny-aware orthologue clustering tool.
Article in Microbial genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections.BMC microbiology · 2021Trial
- Efagins - engineerable agents that evolved independently to target the enterococcal cell wall.bioRxiv : the preprint server for biology · 2026Article
- De novo discovery of conserved gene clusters in microbial genomes with Spacedust.Nature methods · 2025Article
- zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters.Nucleic acids research · 2025Article
- zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters.bioRxiv : the preprint server for biology · 2024Article
- DistinctbioRxiv : the preprint server for biology · 2024Article
- OrthoRefine: automated enhancement of prior ortholog identification via synteny.BMC bioinformatics · 2024Article
- Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance.Genome medicine · 2022Article
- StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities.Genome biology · 2022Article
- A comparative study of pan-genome methods for microbial organisms:Microbial genomics · 2021Article
- Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance.Nature communications · 2021Article
- PanACoTA: a modular tool for massive microbial comparative genomics.NAR genomics and bioinformatics · 2021Article
- Gclust: A Parallel Clustering Tool for Microbial Genomic Data.Genomics, proteomics & bioinformatics · 2019Article
- Defining the core essential genome ofProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Key Transitions in the Evolution of Rapid and Slow GrowingFrontiers in microbiology · 2019Article
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Authors and funding
9 authors.
Funding
Abstract
Accurate orthologue identification is a vital component of bacterial comparative genomic studies, but many popular sequence-similarity-based approaches do not scale well to the large numbers of genomes that are now generated routinely. Furthermore, most approaches do not take gene synteny into account, which is useful information for disentangling paralogues. Here, we present SynerClust, a user-friendly synteny-aware tool based on synergy that can process thousands of genomes. SynerClust was designed to analyse genomes with high levels of local synteny, particularly prokaryotes, which have operon structure. SynerClust's run-time is optimized by selecting cluster representatives at each node in the phylogeny; thus, avoiding the need for exhaustive pairwise similarity searches. In benchmarking against Roary, Hieranoid2, PanX and Reciprocal Best Hit, SynerClust was able to more completely identify sets of core genes for datasets that included diverse strains, while using substantially less memory, and with scalability comparable to the fastest tools. Due to its scalability, ease of installation and use, and suitability for a variety of computing environments, orthogroup clustering using SynerClust will enable many large-scale prokaryotic comparative genomics efforts.
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