Coinfinder: Detecting significant associations and dissociations in pangenomes

Whelan, Fiona Jane; Rusilowicz, Martin; McInerney, James Oscar

Abstract

© 2020 The Authors. 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 homolo-gous 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.

Citation

Whelan, F. J., Rusilowicz, M., & McInerney, J. O. (2020). Coinfinder: Detecting significant associations and dissociations in pangenomes. Microbial Genomics, 6(3), https://doi.org/10.1099/mgen.0.000338

• Journal Article Type: Article
• Acceptance Date: Jan 23, 2020
• Online Publication Date: Feb 25, 2020
• Publication Date: Feb 25, 2020
• Deposit Date: Jul 14, 2020
• Publicly Available Date: Jul 16, 2020
• Journal: Microbial Genomics
• Electronic ISSN: 2057-5858
• Publisher: Microbiology Society
• Peer Reviewed: Peer Reviewed
• Volume: 6
• Issue: 3
• DOI: https://doi.org/10.1099/mgen.0.000338
• Public URL: https://nottingham-repository.worktribe.com/output/4066548
• Publisher URL: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000338#abstract_content