ArticleNucleic acids research2013
CoPAP: Coevolution of presence-absence patterns.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Epistasis and co-adaptation in bacterial genome evolution.Nature reviews. Genetics · 2026Review
- CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset.NAR genomics and bioinformatics · 2025Article
- Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases.eLife · 2023Article
- Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases.bioRxiv : the preprint server for biology · 2023Article
- The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles.Systematic biology · 2023Article
- Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes.BMC bioinformatics · 2023Article
- Signatures of selection in core and accessory genomes indicate different ecological drivers of diversification among Bacillus cereus clades.Molecular ecology · 2022Article
- Inverse Potts model improves accuracy of phylogenetic profiling.Bioinformatics (Oxford, England) · 2022Article
- On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins.PLoS computational biology · 2021Article
- Coinfinder: detecting significant associations and dissociations in pangenomes.Microbial genomics · 2020Article
- Horizontal Gene Transfer as a Source of Conflict and Cooperation in Prokaryotes.Frontiers in microbiology · 2020Article
- A multi-scale coevolutionary approach to predict interactions between protein domains.PLoS computational biology · 2019Article
- Phylogenetic Clustering of Genes Reveals Shared Evolutionary Trajectories and Putative Gene Functions.Genome biology and evolution · 2018Article
- BIS2Analyzer: a server for co-evolution analysis of conserved protein families.Nucleic acids research · 2017Article
- Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires.Nature genetics · 2016Article
- Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2015Article
- Protein complexes in bacteria.PLoS computational biology · 2015Article
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Authors and funding
5 authors.
Funding
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Abstract
Evolutionary analysis of phyletic patterns (phylogenetic profiles) is widely used in biology, representing presence or absence of characters such as genes, restriction sites, introns, indels and methylation sites. The phyletic pattern observed in extant genomes is the result of ancestral gain and loss events along the phylogenetic tree. Here we present CoPAP (coevolution of presence-absence patterns), a user-friendly web server, which performs accurate inference of coevolving characters as manifested by co-occurring gains and losses. CoPAP uses state-of-the-art probabilistic methodologies to infer coevolution and allows for advanced network analysis and visualization. We developed a platform for comparing different algorithms that detect coevolution, which includes simulated data with pairs of coevolving sites and independent sites. Using these simulated data we demonstrate that CoPAP performance is higher than alternative methods. We exemplify CoPAP utility by analyzing coevolution among thousands of bacterial genes across 681 genomes. Clusters of coevolving genes that were detected using our method largely coincide with known biosynthesis pathways and cellular modules, thus exhibiting the capability of CoPAP to infer biologically meaningful interactions. CoPAP is freely available for use at http://copap.tau.ac.il/.
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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.