treeWAS

treeWAS performs phylogeny-aware microbial genome-wide association analysis to identify genotype-phenotype associations while accounting for clonal population structure and homologous recombination.

Key Features:

• Phylogenetic Approach: Employs a phylogeny-aware methodology tailored for microbial GWAS to handle clonal population structure and homologous recombination.
• Robustness to Confounding Effects: Mitigates confounding from population structure and recombination to reduce false positives while maintaining statistical power.
• Versatility with Phenotypes: Applicable to both binary and continuous phenotypes.
• Statistical Power and Specificity: Demonstrated superior power and specificity on simulated data compared with cluster-based and dimension-reduction techniques.

Scientific Applications:

• Neisseria meningitidis studies: Confirmed previously identified penicillin resistance loci and aided discovery of known and novel genetic drivers of disease invasiveness.

Methodology:

Constructs phylogenetic trees that account for evolutionary relationships among microbial strains and performs association analyses that consider genetic background and recombination events.