Coinfinder

Coinfinder identifies significant associations and dissociations among homologous gene families within pangenomes to detect coincident gene pairs that co-occur more frequently than expected and to characterize accessory gene evolutionary dynamics in prokaryotic and eukaryotic organisms.

Key Features:

• Detection of Coincidence: Assesses whether homologous gene families associate or dissociate more often than expected by chance across genomes in a pangenome.
• Phylogenetic Contextualization: Uses a user-supplied phylogenetic tree to evaluate lineage-dependence and ensure identified coincident gene pairs are not explained solely by shared clade membership.
• Multi-language Implementation: Implemented in C++, Python3, and R.
• Output Formats: Generates outputs in text, gexf (Graph Exchange XML Format), and PDF formats.

Scientific Applications:

• Horizontal Gene Transfer: Identifies gene co-occurrence patterns consistent with horizontal gene transfer events.
• Differential Gene Loss: Infers patterns of differential gene loss by detecting non-random dissociations of gene families.
• Selection and Drift on Pangenomes: Examines effects of selection and drift on accessory gene distributions across lineages.
• Functional Relationship Discovery: Suggests functional linkages and evolutionary pressures shaping microbial genomes by identifying genes that co-occur more frequently than expected.

Methodology:

Evaluates co-occurrence of homologous gene families using a phylogenetic framework with a user-supplied tree to assess lineage-dependence and identify associations and dissociations beyond clade presence.