ArticleMicrobial genomics2020
Coinfinder: detecting significant associations and dissociations in pangenomes.
Article in Microbial genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- High-precision binary trait association on phylogenetic trees.Microbial genomics · 2026Article
- Epistasis and co-adaptation in bacterial genome evolution.Nature reviews. Genetics · 2026Review
- Panorama: A robust pangenome-based method for predicting and comparing biological systems across species.PLoS computational biology · 2026Article
- Eco-evolutionary feedbacks drive the co-occurrence of restriction-modification systems and antimicrobial resistance genes in bacteria.PLoS biology · 2026Article
- Comprehensive profiling of insertion sequences and eukaryotic-like transposons across archaeal genomes.BMC genomics · 2026Article
- PyamilySeq: exposing the fragility of conventional gene (re)clustering and prokaryotic pangenomic inference methods.NAR genomics and bioinformatics · 2026Article
- PanForest: predicting genes in genomes using random forests.Bioinformatics (Oxford, England) · 2026Article
- Genomics of Irish swine-derivedMicrobial genomics · 2026Article
- Defence systems drive accessory genome interactions inISME communications · 2026Article
- A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation.PLoS biology · 2025Article
- CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset.NAR genomics and bioinformatics · 2025Article
- Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes.Molecular biology and evolution · 2025Article
- Article
- TheeLife · 2025Article
- A phylogenetic approach to comparative genomics.Nature reviews. Genetics · 2025Review
- Article
- Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.mSystems · 2025Review
- SCARAP: scalable cross-species comparative genomics of prokaryotes.Bioinformatics (Oxford, England) · 2024Article
- Genotypic and phenotypic characterisation of asymptomatic bacteriuria (ABU) isolates displaying bacterial interference against multi-drug resistant uropathogenic E. Coli.Archives of microbiology · 2024Article
- Emergence of potentially disinfection-resistant, naturalized Escherichia coli populations across food- and water-associated engineered environments.Scientific reports · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The accessory genes of prokaryote and eukaryote pangenomes accumulate by horizontal gene transfer, differential gene loss, and the effects of selection and drift. We have developed Coinfinder, a software program that assesses whether sets of homologous genes (gene families) in pangenomes associate or dissociate with each other (i.e. are 'coincident') more often than would be expected by chance. Coinfinder employs a user-supplied phylogenetic tree in order to assess the lineage-dependence (i.e. the phylogenetic distribution) of each accessory gene, allowing Coinfinder to focus on coincident gene pairs whose joint presence is not simply because they happened to appear in the same clade, but rather that they tend to appear together more often than expected across the phylogeny. Coinfinder is implemented in C++, Python3 and R and is freely available under the GNU license from https://github.com/fwhelan/coinfinder.
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Registered trials
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.