Coinfinder: Detecting Significant Associations and Dissociations in Pangenomes

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

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 GPU license from https://github.com/fwhelan/coinfinder.

Citation

Whelan, F. J., Rusilowicz, M., & McInerney, J. O. Coinfinder: Detecting Significant Associations and Dissociations in Pangenomes

• Deposit Date: Oct 29, 2022
• Publicly Available Date: Nov 1, 2022
• Public URL: https://nottingham-repository.worktribe.com/output/3612066
• Publisher URL: https://www.biorxiv.org/content/10.1101/859371v1