CALANGO

CALANGO performs phylogeny-aware comparative genomics to associate genomic annotation terms (e.g., Pfam IDs, GO terms, superfamilies) with quantitative or rank phenotypes across species and to detect functional molecular convergences and homologous regions linked to those phenotypes.

Key Features:

• Phylogeny-Aware Analysis: Incorporates phylogenetic information to account for evolutionary relationships when analyzing comparative genomic data.
• Quantitative/Rank Variable Integration: Associates annotation terms such as Pfam IDs, GO terms, or superfamilies with quantitative variables (for example, cell type numbers, genome size, or genomic element density) or rank-ordered traits across species.
• Detection of Functional Molecular Convergence: Identifies functional molecular convergences and homologous regions associated with quantitative genotypes and phenotypes across taxa.
• Statistically Sound Discoveries: Supports discovery of statistically robust phenotype–genotype associations to aid interpretation of potential causal links.
• Counterfactual Analysis Capability: Enables exploration of counterfactual scenarios in observed data associations to investigate alternative explanations.

Scientific Applications:

• Microbial pathogenicity analysis: Revealed a potential relationship between prophage density and pathogenicity in Escherichia coli.
• Plant evolutionary biology: Identified a link between maximum height in angiosperms and the expansion of the self-incompatibility system, suggesting taller species may offset slower molecular evolution associated with longer generation times.

Methodology:

Performs phylogeny-aware statistical association of genomic annotation terms (e.g., Pfam IDs, GO terms, superfamilies) with quantitative or rank variables by leveraging phylogenetic data and genomic annotations to identify functional molecular convergences and homologous regions.